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. Author manuscript; available in PMC: 2019 Jan 1.
Published in final edited form as: Cancer Epidemiol Biomarkers Prev. 2017 Nov 17;27(1):75–85. doi: 10.1158/1055-9965.EPI-17-0516

Table 2.

The 20 variant groups (33 variants) pleiotropic for cancer risk within the same ethnic group.

Variant
group		 Region Cancer sites Variant rs
number		 LD (R2)a Cancer site
associated with
the variant		 EAb EAFb P-valuec ORb 95%
confidence
interval of
ORb 		Ancestry
of the
discovery
sampled 		Mapped
genee 		PubMed
ID of the
study
rs4245739 1q32.1 Breast, Prostate rs4245739 1 Breast C 0.26 2E-12 1.14 [1.10–1.18] European MDM4 23535733
rs4245739 1 Prostate C 0.25 2E-11 0.91 [0.88–0.95] European MDM4 23535732
rs10936599, rs12638862, rs12696304 3q26.2 Colon & rectum, Leukemia, Multiple myeloma, Skin, Urinary bladder rs12638862 1 (Ref) Multiple myeloma A 0.74 2E-06 1.37 [1.20–1.56] European 4.9kb 3' of TERC 23502783
rs12696304 0.945 Skin C 0.73 3E-07 1.10 [NR] European 1.1kb 3′ of TERC 26237428
rs10936599 0.928 Urinary bladder C 0.76 5E-09 1.18 [1.11–1.23] European MYNN 24163127
rs10936599 0.928 Colon & rectum C 0.75 3E-08 1.08 [1.04–1.10] European MYNN 20972440
rs10936599 0.928 Leukemia C 0.75 2E-09 1.26 [1.17–1.35] European MYNN 24292274
rs10936599 0.928 Multiple myeloma C 0.80 9E-14 1.26 [1.18–1.33] European MYNN 23955597
rs10069690 5p15.33 Breast, Ovary rs10069690 1 Breastf T 0.32 5E-12 1.15 [1.11–1.20] European TERT 23535733
rs10069690 1 Ovary T 0.26 9E-09 1.14 [1.10–1.19] European TERT 25581431
rs2736100 5p15.33 Brain, Lung, Testis rs2736100 1 Brain G 0.49 2E-17 1.27 [1.19–1.37] European TERT 19578367
rs2736100 1 Lungf G 0.50 2E-10 1.12 [1.08–1.16] European TERT 19836008
rs2736100 1 Testis G 0.51 8E-15 0.75 [0.67–0.85] European TERT 20543847
rs31489, rs31490, rs401681, rs4975616 5p15.33 Leukemia, Lung, Pancreas, Skin, Urinary bladder rs4975616 1 (Ref) Lung NR NR 3E-09 1.15 [1.10–1.20] European 2.2kb 3' of CLPTM1L 19654303
rs401681g 0.849 Urinary bladder C 0.54 4E-11 1.12 [1.08–1.16] European CLPTM1L 24163127
rs401681 0.849 Lung C 0.57 8E-09 1.15 [1.09–1.19] European CLPTM1L 18978787
rs401681 0.849 Skin C 0.55 9E-13 1.21 [NR] European CLPTM1L 25855136
rs31489 0.735h Lung C 0.59 2E-10 1.12 [1.09–1.16] European CLPTM1L 19836008
rs31490 0.849 Leukemia A 0.43 2E-07 1.18 [1.11–1.26] European CLPTM1L 24292274
rs31490 0.849 Pancreas A 0.44 2E-11 1.20 [1.14–1.27] European CLPTM1L 25086665
rs3777204, rs56219066 5q15 Salivary gland, Multiple myeloma rs3777204i 1 (Ref) Salivary gland C 0.29 1E-07 1.86 [1.48–2.34] European ELL2 j 25823930
rs56219066 0.971 Multiple myeloma T 0.71 1E-09 1.25 [1.16–1.34] European ELL2 j 26007630
rs2494938 6p21.1 Lung, Stomach rs2494938 1 Lung A 0.23 2E-06 1.15 [1.08–1.22] East Asian LRFN2 23103227
rs2494938 1 Stomach A 0.23 5E-09 1.18 [1.12–1.25] East Asian LRFN2 23103227
rs2285947 7p15.3 Esophagus, Lung, Stomach rs2285947 1 Esophagus A 0.27 3E-06 1.14 [1.08–1.21] East Asian DNAH11 23103227
rs2285947 1 Lung A 0.26 2E-08 1.17 [1.11–1.24] East Asian DNAH11 23103227
rs2285947 1 Stomach A 0.27 1E-06 1.14 [1.08–1.21] East Asian DNAH11 23103227
rs10505477, rs6983267 8q24.21 Colon & rectum, Prostate rs10505477 1 (Ref) Colon & rectum T 0.54 8E-13 1.20 [NR] European 20kb 5' of POU5F1B 24737748
rs10505477 1 (Ref) Prostate T 0.49 9E-09 1.39 [1.28–1.50] European 20kb 5' of POU5F1B 24740154
rs6983267 0.916 Colon & rectumf G 0.49 1E-14 1.27 [1.16–1.39] European 15kb 5' of POU5F1B 17618284
rs6983267 0.916 Prostatef G 0.50 4E-15 1.34 [1.25–1.43] European 15kb 5' of POU5F1B 24753544
rs2294008 8q24.3 Stomach, Urinary bladder rs2294008 1 Urinary bladder T 0.46 3E-15 1.13 [1.10–1.16] European PSCA 24163127
rs2294008 1 Stomach T 0.47 2E-07 1.21 [NR] European PSCA 26098866
rs11012732, rs1243180 10p12.31 Brain, Ovary rs11012732 1 (Ref) Brain A 0.32 2E-14 1.46 [1.32–1.61] European MLLT10 21804547
rs1243180 0.858 Ovary A 0.31 1E-09 1.10 [1.06–1.14] European MLLT10 25581431
rs174537, rs174549 11q12.2 Colon & rectum, Larynx rs174537 1 (Ref) Colon & rectum G 0.59 9E-21 1.16 [1.12–1.19] East Asian MYRF 24836286
rs174549 0.923 Larynx A 0.59 1E-20 1.37 [1.28–1.47] East Asian FADS1 25194280
rs735665 11q24.1 Leukemia, Lymphoma rs735665 1 Leukemia A 0.19 4E-39 1.62 [NR] European 35kb 5' of GRAMD1B 23770605
rs735665 1 Lymphoma A 0.21 4E-09 1.81 [1.50–2.20] European 35kb 5' of GRAMD1B 20639881
rs11571833 13q13.1 Breast, Lung rs11571833 1 Breast T 0.01 5E-08 1.26 [1.14–1.39] European BRCA2 23535729
rs11571833 1 Lung T 0.01 5E-20 2.47 [2.03–3.00] European BRCA2 24880342
rs35158985, rs9929218 16q22.1 Colon & rectum, Skin rs35158985 1 (Ref) Skin G 0.30 3E-07 1.10 [NR] European CDH1 26237428
rs9929218 0.861 Colon & rectum G 0.29 1E-08 1.10 [1.06–1.12] European CDH1 19011631
rs4430796, rs8064454 17q12 Endometrium, Prostate rs4430796 1 (Ref) Endometrium A 0.52 7E-10 1.19 [1.12–1.27] European HNF1B 21499250
rs4430796 1 (Ref) Prostatef A 0.49 1E-11 1.22 [1.15–1.30] European HNF1B 17603485
rs8064454 0.949 Prostate C 0.52 8E-29 1.24 [1.19–1.29] European HNF1B 25939597
rs7501939, rs757210 17q12 Prostate, Testis rs757210 1 (Ref) Ovary G 0.37 8E-10 1.12 [1.08–1.17] European HNF1B 23535730
rs7501939 0.8 Prostatef NR NR 3E-18 NR [NR] European HNF1B 19767753
rs7501939 0.8 Testis C 0.62 1E-09 1.28 [1.19–1.39] European HNF1B 25877299
rs17749561, rs4987855 18q21.33 Leukemia, Lymphoma rs17749561 1 (Ref) Lymphoma G 0.91 8E-10 1.34 [1.22–1.47] European 7.4kb 3' of BCL2 25279986
rs4987855 0.951 Leukemia G 0.91 3E-12 1.47 [1.32–1.61] European BCL2 23770605
rs8170 19p13.11 Breast, Ovary rs8170 1 Breast C 0.48 4E-13 1.19 [1.14–1.25] European BABAM1 23544013
rs8170 1 Ovary NR 0.19 3E-14 1.19 [1.14–1.25] European BABAM1 23535730
rs2363956 19p13.11 Breast, Ovary rs2363956 1 Breast NR NR 2E-08 1.22 [1.14–1.30] European ANKLE1 24325915
rs2363956 1 Ovary T 0.43 1E-07 1.10 [1.06–1.15] European ANKLE1 20852633
a

Linkage disequilibrium (LD).

b

Effect allele (EA), effect allele frequency (EAF), odds ratio (OR), 95% confidence interval of OR were retrieved from the GWAS Catalog. We described the effect allele in RefSNP orientation as dbSNP did. We also manually reviewed the original publications and dbSNP to fill in the information not reported in the GWAS Catalog. NR: Information not reported in either the GWAS Catalog or the original publications of the study, and not able to be retrieved from dbSNP.

c

For the same variant-cancer risk association repeatedly identified by multiple studies, the one with the smallest p-value and/or identified by the most recent study was reported in this table.

d

Clustering of variants into variant groups based on pairwise LD was performed within each of the 17 ethnic groups shown in Table 2, and only the variant groups in the European and East Asian population showed pleiotropic effects for cancer risk.

e

For variants located within a gene, the gene symbol was reported directly. For intergenic variants, distance and direction to the closest gene were reported.

f

Statistically significant association was also observed in other populations:

rs10069690 and breast cancer in European and African American/Afro-Caribbean (PubMed ID: 22037553).

rs2736100 and lung cancer in East Asian (PubMed ID: 21725308).

rs6983267 and colorectal cancer in East Asian (PubMed ID: 24836286); rs6983267 and prostate cancer in a sample of European, African American/Afro-Caribbean, East Asian, Hispanic/Latin American (PubMed ID: 26034056).

rs4430796 and prostate cancer in East Asian (PubMed ID: 26443449).

rs7501939 and prostate cancer in East Asian (PubMed ID: 20676098), and in a sample of European, African American/Afro-Caribbean, East Asian, Hispanic/Latin American (PubMed ID: 26034056).

g

Variant rs401681 has been associated with pancreatic cancer in a sample of European, African unspecified, Asian unspecified, Hispanic/Latin American (PubMed ID: 26098869) and another sample of European and East Asian (PubMed ID: 20101243).

h

Variant rs31489 is in high LD with rs31490 (R2 = 0.874) and rs401681 (R2 = 0.814).

i

Variant rs3777204 was shown as exm2265979 in the original publication.

j

ELL2 is a pleiotropic gene that is novel to this study.