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. 2019 Dec 9;28:104962. doi: 10.1016/j.dib.2019.104962

Dataset of allele and genotype frequencies of five polymorphisms candidate genes analyzed for association with body mass index in Russian women

Evgeny Reshetnikov a,∗, Maria Abramova a, Irina Ponomarenko a, Alexey Polonikov b, Irina Verzilina a, Inna Sorokina a, Inna Aristova a, Anna Yermachenko c,d, Volodymyr Dvornyk e, Mikhail Churnosov a
PMCID: PMC6931107  PMID: 31890803

Abstract

Data on the allele and genotype frequencies of the five single nucleotide polymorphisms (SNPs) 5 genes - rs1514175 TNNI3K, rs713586 RBJ, rs887912 FANCL, rs2241423 MAP2K5, rs12444979 GPRC5B in Russian women are presented. Several genome-wide association studies identified these SNPs could be significant genetic markers associated with body mass index (BMI). Standard methods were used for collecting of the anthropometric characteristics (height and weight). We calculated the frequencies of alleles and genotypes of five SNPs in 5 groups: all samples, underweight (BMI<18.50), normal weight (18.50–24.99), overweight (25.00–29.99), obese (>30.00).

Keywords: Single nucleotide polymorphism, Body mass index, Women, TNNI3K, RBJ, FANCL, MAP2K5, GPRC5B

Specifications Table

Subject area Biology
More specific subject area Genetics
Type of data Table
How data was acquired MALDI/TOF mass spectrometry using Sequenom MassARRAY 4.0 platform (Agena Bioscience™)
Data format Raw and analyzed data
Experimental factors Total genomic DNA was isolated from buffy coat using the standard phenol-chloroform method.
Experimental features DNA samples were genotyped using the Sequenom MassARRAY® iPLEX platform, which is based on MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry
Data source location Belgorod, Russia
Data accessibility The data is available with this article
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Value of the Data
  • •

    The frequencies of alleles and genotypes of rs1514175 TNNI3K, rs713586 RBJ, rs887912 FANCL, rs2241423 MAP2K5, and rs12444979 GPRC5B among Russian women with different body mass index (underweight, normal weight, overweight, obesity) vary, but do not differ significantly.

  • •

    The genetic polymorphisms in TNNI3K, RBJ, FANCL, MAP2K5, GPRC5B genes may play a role in body mass index.

  • •

    The data on the allele and genotype frequencies are an important resource for understanding genetic structure of different populations.

  • •

    The data can be used to study a genetic basis of body mass index and BMI-associated multifactorial diseases (obesity, arterial hypertension, metabolic syndrome, stroke, coronary artery disease, uterine leiomyoma, and the others) in various populations.

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1. Data

The dataset represents the raw data (supplementary Table), frequencies of alleles and genotypes for five single nucleotide polymorphisms (SNPs) of 5 genes, rs1514175 TNNI3K, rs713586 RBJ, rs887912 FANCL, rs2241423 MAP2K5, and rs12444979 GPRC5B in Russian women (Table 1). These SNPs were associated with body mass index (BMI) in previously published genome-wide and candidate gene association studies [[1], [2], [3], [4], [5], [6], [7], [8], [9], [10]]. The dataset frequencies of the SNP alleles and genotypes were divided into five groups according to the BMI of the participants: all samples, underweight (BMI<18.50), normal weight (18.50–24.99), overweight (25.00–29.99), and obese (>30.00). No significant differences in the allele and genotype frequencies between the groups with underweight (BMI<18.50), normal weight (18.50–24.99), overweight (25.00–29.99) and obese (>30.00) (p > 0.05) were determined.

Table 1.

The frequencies of alleles and genotypes for single nucleotide polymorphisms (SNPs) rs1514175 TNNI3K, rs713586 RBJ, rs887912 FANCL, rs2241423 MAP2K5, rs12444979 GPRC5B in the sample of Russian women.

SNP genotype or allele All (n = 716)
 Body mass index
n frequency Mean, kg/m2 underweight (BMI<18.50) (n = 40)
 normal weight (18.50–24.99) (n = 445)
 overweight (25.00–29.99) (n = 159)
 obese (>30.00) (n = 72)
n frequency n frequency n frequency n frequency
rs1514175 TNNI3K
CC 275 0.3841 23.84 ± 4.46 21 0.5250 173 0.3888 59 0.3710 22 0.3056
CT 331 0.4623 24.16 ± 4.37 11 0.2750 206 0.4629 70 0.4403 44 0.6111
TT 110 0.1536 23.13 ± 3.70 8 0.2000 66 0.1483 30 0.1887 6 0.0833
C 881 0.6152 – 53 0.6625 552 0.6202 188 0.5912 88 0.6111
T 551 0.3848 – 27 0.3375 338 0.3798 130 0.4088 56 0.3889
rs713586 RBJ
TT 238 0.3324 23.61 ± 4.13 18 0.4500 146 0.3281 49 0.3082 25 0.3472
TC 340 0.4749 24.08 ± 4.65 18 0.4500 212 0.4764 73 0.4591 37 0.5139
CC 138 0.1927 23.92 ± 3.74 4 0.1000 87 0.1955 37 0.2327 10 0.1389
T 816 0.5698 – 54 0.6750 504 0.5663 171 0.5377 87 0.6042
C 616 0.4302 – 26 0.3250 386 0.4337 147 0.4623 57 0.3958
rs887912 FANCL
GG 437 0.6103 23.96 ± 4.47 27 0.6750 270 0.6067 95 0.5975 45 0.6250
GA 238 0.3324 23.68 ± 4.19 12 0.3000 152 0.3416 50 0.3145 24 0.3333
AA 41 0.0573 24.11 ± 3.30 1 0.0250 23 0.0517 14 0.0880 3 0.0417
G 1112 0.7765 – 66 0.8250 692 0.7775 240 0.7547 114 0.7917
A 320 0.2235 – 14 0.1750 198 0.2225 78 0.2453 30 0.2083
rs2241423 MAP2K5
GG 474 0.6620 23.81 ± 4.11 27 0.6750 288 0.6471 115 0.7233 44 0.6111
GA 213 0.2975 23.93 ± 4.65 11 0.2750 141 0.3169 37 0.2327 24 0.3333
AA 29 0.0405 24.72 ± 5.17 2 0.0500 16 0.0360 7 0.0440 4 0.0556
G 1161 0.8108 – 65 0.8125 717 0.8056 267 0.8396 112 0.7778
A 271 0.1892 – 15 0.1875 173 0.1944 51 0.1604 32 0.2222
rs12444979 GPRC5B
CC 524 0.7318 23.99 ± 4.36 29 0.7250 320 0.7191 118 0.7421 57 0.7917
CT 175 0.2444 23.56 ± 4.25 11 0.2750 114 0.2562 37 0.2327 13 0.1805
TT 17 0.0238 23.96 ± 3.79 – – 11 0.0247 4 0.0252 2 0.0278
C 1223 0.8541 – 69 0.8625 754 0.8472 273 0.8585 127 0.8819
T 209 0.1459 – 11 0.1375 136 0.1528 45 0.1415 17 0.1181
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2. Experimental design, materials, and methods

2.1. Study subjects

From 2009 to 2013, women referred to the Perinatal Centre of the Belgorod Regional Clinical Hospital of St. Joasaph were enrolled. The participants were unrelated Russian women born in Central Russia [11]. Some exclusion criteria were adopted: benign tumors and hyperplastic disorders of the reproductive organs (endometriosis, leiomyoma, and endometrial hyperplasia), malignant tumors of a small pelvis and breast, severe autoimmune diseases, chronic severe diseases of the vital organs (heart, respiratory or renal failure). A total of 716 women met the criteria. This study was approved by the Regional Ethics Committee of Belgorod State University and informed consents were obtained from all participants.

The anthropometric characteristics were obtained by standard methods [12]: a portable stadiometer was used for measurement of height; weight was measured in an upright position, using a calibrated balance beam scale. 5 groups were formed according to BMI: total sample set, sample set with the underweight (BMI<18.50), normal weight (18.50–24.99), overweight (25.00–29.99) and obese (>30.00).

2.2. Blood sample collection and DNA handling

Whole blood specimens were collected from each participant using a plastic tubes (Vacutainer®) containing 0.5 M EDTA solution (рН = 8.0) and genomic DNA was isolated from peripheral blood leukocytes using the standard phenol-chloroform method. The isolated DNA was stored at −80°С.

2.3. SNP selection

Five SNPs in five genes, rs1514175 TNNI3K, rs713586 RBJ, rs887912 FANCL, rs2241423 MAP2K5, and rs12444979 GPRC5B were selected for the analysis according to the following criteria [13]: 1) Previously reported genome-wide and candidate genes associations with body mass index (BMI) and obesity, 2) Regulatory potential (regSNP), 3) Effect on gene expression (eSNP), and 4) Tag value (tagSNP) and 5) MAF > 5%.

The selected loci were associated with BMI in previously published genome-wide and candidate gene association studies (Table 2) and have functional significance: all SNPs appear to have a significant regulatory potential (Table 3) (determined using the online tools HaploReg, v4.1 update November 05, 2015, https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php) and 4 SNPs to influence gene expression level (Table 4) (determined using the GTExportal data, http://www.gtexportal.org/).

Table 2.

The literature data about associations of the studied polymorphisms with body mass index and obesity.

Chr (1) SNP (2 Gene/Region Phenotype Association (significance) (associated allele/genotype) Reference
1 rs1514175 TNNI3K Body mass index 0.07 kg/m2(p = 8 x10−14) (А) [1]
Body mass index 0.06 unit (p = 3 x10−11) (А) [3]
Body mass index 0.20 kg/m2 (p = 7.7 × 10−4) (A) [4]
2 rs713586 RBJ Body mass index 0.14 kg/m2(p = 6 x10−22) (С) [1]
2 rs887912 FANCL Body mass index 0.1 kg/m2(p = 2 x10−12) (T) [1]
Obesity (class I) OR = 1.07 (p = 1 x10−10) (T) [2]
Obesity (class II) OR = 1.1 (p = 6 x10−9) (T) [2]
15 rs2241423 MAP2K5 Body mass index 0.13 kg/m2(p = 1 x10−18) (G)
Obesity OR = 0.79 (p = 0.029) (A) [1]
Body mass index −0.092 unit (p = 0.028) (A) [5]
Children obesity (p < 0.005) [5]
Obesity OR = 1.34 (0.001) (G) [6]
Adulthood body mass index (p < 0.05) [7]
Body mass index 0.11 kg/m2 (p = 0.028) (G) [8]
16 rs12444979 GPRC5B Body mass index 0.17 kg/m2(p = 3 x10−21) (C) [1]
Body mass index (p < 0.05) [9]
Body mass index (EA) (p = 0.014) [10]
Body fat mass (EA) (p = 0.002) [10]
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Note: The data from the GWAS are shown in bold.

Table 3.

Regulatory effects of the 5 SNPs of the TNNI3K, RBJ, FANCL, MAP2K5, and GPRC5B genes (HaploReg, v4.1, update November 05, 2015) (https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php).

chr pos (hg38) variant Reference allele Alternative allele AFR
 AMR
 ASN
 EUR
 SiPhy
 Promoter
 Enhancer
 DNAse Proteins
 Motifs
 NHGRI/EBI
 GRASP QTL
 Selected eQTL
 GENCODE
 dbSNP
freq freq freq freq cons histone marks histone marks bound changed GWAS hits hits hits genes func annot
1 74525960 rs1514175 A G 0.31 0.42 0.2 0.56 ESC, ESDR, IPSC COMP1,ERalpha-a 2 hits 2 hits FPGT-TNNI3K intronic
2 24935139 rs713586 T C 0.9 0.43 0.46 0.46 Pbx3,SP2,TATA 1 hit 3 hits 34 hits 8.5kb 3′ of DNAJC27
2 59075742 rs887912 T C 0.94 0.83 1 0.73 Hoxa5,Znf143 3 hits 12kb 3′ of AC007092.1
15 67794500 rs2241423 G A 0.4 0.43 0.6 0.23 IPSC 1 hit 1 hit 16 hits MAP2K5 intronic
16 19922278 rs12444979 C T 0.09 0.06 0 0.12 LBP-1 1 hit 70 hits 32kb 3′ of AC134300.1
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Table 4.

The cis-eQTL values of the 5 SNPs of the TNNI3K, RBJ, FANCL, MAP2K5, and GPRC5B genes (according to Genotype-Tissue Expression (GTEx) (http://www.gtexportal.org/)).

chr SNP Gene Gene expression Reference allele Alternative allele Effect Size (β) P-Value Tissue
1 rs1514175 TNNI3K LRRIQ3 A G 0.25 0.0000045 Thyroid
2 rs713586 RBJ ADCY3 T C 0.31 0.00000018 Skin - Sun Exposed (Lower leg)
rs713586 RBJ CENPO T C 0.71 2.9E-38 Whole Blood
rs713586 RBJ ADCY3 T C 0.51 5.3E-22 Whole Blood
rs713586 RBJ ADCY3 T C −0.23 0.0000000000000063 Nerve - Tibial
rs713586 RBJ CENPO T C 0.28 0.00000000000031 Artery - Tibial
rs713586 RBJ DNAJC27 T C −0.2 0.00000000012 Nerve - Tibial
rs713586 RBJ DNAJC27-AS1 T C 0.29 0.0000000003 Whole Blood
rs713586 RBJ DNAJC27-AS1 T C −0.27 0.0000000014 Esophagus - Muscularis
rs713586 RBJ CENPO T C −0.39 0.0000000042 Brain - Cerebellum
rs713586 RBJ ADCY3 T C 0.23 0.0000000091 Artery - Tibial
rs713586 RBJ ADCY3 T C 0.18 0.000000014 Adipose - Subcutaneous
rs713586 RBJ CENPO T C −0.41 0.00000015 Cells - EBV-transformed lymphocytes
rs713586 RBJ ADCY3 T C 0.23 0.00000024 Lung
rs713586 RBJ ADCY3 T C 0.18 0.0000006 Adipose - Visceral (Omentum)
rs713586 RBJ CENPO T C −0.15 0.00000079 Skin - Sun Exposed (Lower leg)
rs713586 RBJ CENPO T C 0.18 0.0000011 Adipose - Subcutaneous
rs713586 RBJ DNAJC27-AS1 T C 0.23 0.0000015 Adipose - Visceral (Omentum)
rs713586 RBJ ADCY3 T C −0.33 0.0000026 Pituitary
rs713586 RBJ DNAJC27-AS1 T C −0.14 0.000004 Skin - Not Sun Exposed (Suprapubic)
rs713586 RBJ ADCY3 T C −0.15 0.000016 Nerve - Tibial
rs713586 RBJ EFR3B T C 0.19 0.000031 Lung
rs713586 RBJ POMC T C −0.21 0.000031 Heart - Atrial Appendage
15 rs2241423 MAP2K5 MAP2K5 G A −0.32 4.1E-19 Artery - Tibial
rs2241423 MAP2K5 MAP2K5 G A −0.4 0.0000000000000029 Heart - Atrial Appendage
rs2241423 MAP2K5 MAP2K5 G A −0.32 0.000000000000012 Adipose - Subcutaneous
rs2241423 MAP2K5 MAP2K5 G A −0.27 0.0000000000001 Thyroid
rs2241423 MAP2K5 SKOR1 G A −0.3 0.0000000000019 Lung
rs2241423 MAP2K5 SKOR1 G A −0.32 0.0000000000035 Thyroid
rs2241423 MAP2K5 SKOR1 G A −0.3 0.000000000014 Muscle - Skeletal
rs2241423 MAP2K5 MAP2K5 G A −0.26 0.000000000015 Whole Blood
rs2241423 MAP2K5 SKOR1 G A −0.4 0.000000000073 Heart - Left Ventricle
rs2241423 MAP2K5 SKOR1 G A −0.29 0.00000000021 Adipose - Subcutaneous
rs2241423 MAP2K5 SKOR1 G A −0.35 0.00000000037 Adipose - Visceral (Omentum)
rs2241423 MAP2K5 MAP2K5 G A −0.28 0.00000000092 Esophagus - Muscularis
rs2241423 MAP2K5 SKOR1 G A −0.26 0.0000000014 Artery - Tibial
rs2241423 MAP2K5 SKOR1 G A −0.23 0.0000000062 Skin - Sun Exposed (Lower leg)
rs2241423 MAP2K5 MAP2K5 G A −0.22 0.0000000094 Lung
rs2241423 MAP2K5 MAP2K5 G A −0.29 0.000000011 Artery - Aorta
rs2241423 MAP2K5 SKOR1 G A −0.25 0.000000019 Skin - Not Sun Exposed (Suprapubic)
rs2241423 MAP2K5 MAP2K5 G A −0.27 0.000000054 Nerve - Tibial
rs2241423 MAP2K5 SKOR1 G A −0.2 0.000000095 Nerve - Tibial
rs2241423 MAP2K5 SKOR1 G A −0.32 0.00000011 Artery - Aorta
rs2241423 MAP2K5 MAP2K5 G A −0.27 0.00000012 Adipose - Visceral (Omentum)
rs2241423 MAP2K5 SKOR1 G A −0.48 0.00000013 Pituitary
rs2241423 MAP2K5 SKOR1 G A −0.3 0.00000013 Breast - Mammary Tissue
rs2241423 MAP2K5 SKOR1 G A −0.24 0.00000018 Esophagus - Muscularis
rs2241423 MAP2K5 MAP2K5 G A −0.25 0.00000019 Breast - Mammary Tissue
rs2241423 MAP2K5 MAP2K5 G A −0.23 0.0000009 Heart - Left Ventricle
rs2241423 MAP2K5 SKOR1 G A −0.29 0.0000063 Esophagus - Gastroesophageal Junction
rs2241423 MAP2K5 SKOR1 G A −0.51 0.000011 Ovary
rs2241423 MAP2K5 SKOR1 G A −0.25 0.000012 Colon - Sigmoid
rs2241423 MAP2K5 MAP2K5 G A −0.27 0.000013 Esophagus - Gastroesophageal Junction
rs2241423 MAP2K5 SKOR1 G A −0.2 0.000016 Colon - Transverse
rs2241423 MAP2K5 MAP2K5 G A −0.38 0.000017 Pituitary
rs2241423 MAP2K5 RP11-34F13.2 G A −0.29 0.00004 Thyroid
16 rs12444979 GPRC5B KNOP1 C T 0.64 0.00000000000037 Adipose - Subcutaneous
rs12444979 GPRC5B KNOP1 C T 0.81 0.00000000000000049 Adipose - Visceral (Omentum)
rs12444979 GPRC5B KNOP1 C T 0.66 0.00000000012 Adrenal Gland
rs12444979 GPRC5B KNOP1 C T 0.78 0.000000000000000043 Artery - Aorta
rs12444979 GPRC5B KNOP1 C T 0.67 0.0000000033 Artery - Coronary
rs12444979 GPRC5B KNOP1 C T 0.43 0.0000026 Artery - Tibial
rs12444979 GPRC5B KNOP1 C T 0.77 0.0000067 Brain - Cerebellum
rs12444979 GPRC5B KNOP1 C T 0.89 0.0000000056 Brain - Hypothalamus
rs12444979 GPRC5B KNOP1 C T 0.82 0.0000009 Brain - Nucleus accumbens (basal ganglia)
rs12444979 GPRC5B KNOP1 C T 0.81 0.00000000000071 Breast - Mammary Tissue
rs12444979 GPRC5B KNOP1 C T 0.73 0.0000015 Cells - EBV-transformed lymphocytes
rs12444979 GPRC5B KNOP1 C T 0.69 0.000000062 Colon - Sigmoid
rs12444979 GPRC5B KNOP1 C T 0.51 0.0000000005 Colon - Transverse
rs12444979 GPRC5B KNOP1 C T 0.89 0.00000000000000071 Esophagus - Gastroesophageal Junction
rs12444979 GPRC5B KNOP1 C T 0.58 0.00000000000000021 Esophagus - Mucosa
rs12444979 GPRC5B KNOP1 C T 0.75 1.6E-19 Esophagus - Muscularis
rs12444979 GPRC5B KNOP1 C T 0.73 0.000000005 Heart - Atrial Appendage
rs12444979 GPRC5B KNOP1 C T 0.56 0.00000035 Heart - Left Ventricle
rs12444979 GPRC5B KNOP1 C T 0.65 0.00000000000000011 Lung
rs12444979 GPRC5B KNOP1 C T 0.73 2.00E-20 Muscle - Skeletal
rs12444979 GPRC5B KNOP1 C T 0.91 0.00000000000000013 Nerve - Tibial
rs12444979 GPRC5B KNOP1 C T 1 0.000000042 Ovary
rs12444979 GPRC5B KNOP1 C T 1 0.000000000000029 Pancreas
rs12444979 GPRC5B KNOP1 C T 0.92 0.000000000000016 Skin - Not Sun Exposed (Suprapubic)
rs12444979 GPRC5B KNOP1 C T 0.79 4.1E-21 Skin - Sun Exposed (Lower leg)
rs12444979 GPRC5B KNOP1 C T 0.95 0.000000059 Spleen
rs12444979 GPRC5B KNOP1 C T 0.67 0.000000000000019 Stomach
rs12444979 GPRC5B KNOP1 C T 0.55 0.000000000058 Testis
rs12444979 GPRC5B KNOP1 C T 0.58 0.000000000006 Thyroid
rs12444979 GPRC5B KNOP1 C T 0.77 0.0000015 Vagina
rs12444979 GPRC5B KNOP1 C T 0.35 0.000011 Whole Blood
rs12444979 GPRC5B GPRC5B C T −0.25 0.000046 Adipose - Subcutaneous
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2.4. SNP genotyping

DNA samples were genotyped using the Sequenom MassARRAY® iPLEX platform. The procedure for DNA sample preparation and data quality control are described elsewhere [12].

2.5. Statistical analysis

All polymorphisms were checked for their correspondence to the Hardy-Weinberg equilibrium (HWE) using the chi-square test. Differences in allele and genotype frequencies between the groups of underweight (BMI<18.50), normal weight (18.50–24.99), overweight (25.00–29.99), and obese (>30.00) women were determined using the Kruskall-Wallis test.

Acknowledgements

This is a self-funded work with no external sponsorship.

Footnotes

Appendix A

Supplementary data to this article can be found online at https://doi.org/10.1016/j.dib.2019.104962.

Conflict of Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Appendix A. Supplementary data

The following is the Supplementary data to this article:

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