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. Author manuscript; available in PMC: 2023 Nov 17.
Published in final edited form as: Biochim Biophys Acta Mol Cell Biol Lipids. 2020 Feb 5;1865(11):158653. doi: 10.1016/j.bbalip.2020.158653

Table 1.

Previously conducted studies of BCO1 SNPs with significant relationships to carotenoid and retinol concentrations and/or disease

SNP Accession Number Location relative to BCO11 Alleles Second Allele Frequency Second Allele Effect2 Measure(s) Population Studied
rs48892864 upstream C/T 0.50 + circulating BC, AC NHS [53]
rs4889293 within (intron variant) C/G 0.42 + circulating AC NHS [53]
rs6420424 upstream G/A 0.34, 0.49 + circulating BC inCHIANTI, WHAS [49]
G/A 0.45 - post-prandial ROL/BC Healthy UK women (n = 28) [58]
rs65648513,4 upstream T/G 0.36, 0.48, 0.39 + circulating BC, AC, LYC inCHIANTI, WHAS, ATBC (placebo arm only)[49]
T/G 0.36, 0.48, 0.39 - circulating LUT, ZEA inCHIANTI, WHAS, ATBC (placebo arm only)[49]
T/G 0.50 + circulating BC, AC, BCrypt NHS [53]
T/G 0.50 - circulating LUT/ZEA NHS [53]
T/G 0.48 - post-prandial ROL/BC Healthy UK women (n = 28) [58]
T/G not available + BC uptake after 54 d supplementation Healthy UK women (n=85)[59]
T/G 0.82 + circulating BC, daily BC intake Healthy Japanese men & women (n=92)[50]
C/A 0.49 + circulating LUT+ZEA CAREDS postmenopausal women (n=1663) [52]
T/G 0.57 + circulating LYC after ~25 days tomato juice supplementation; prostate BC and LYC American men with prostate cancer (n=47)[60]
rs6564863 within (intron variant) G/A 0.34 + MPOD CAREDS postmenopausal women (n=1585) [65]
rs7196470 downstream C/A 0.24 - post-prandial BC Healthy French men (n = 33)[54]
rs7500996 within (intron variant) A/G 0.18 + circulating LUT+ZEA CAREDS postmenopausal women (n=1663) [52]
rs7501331 within (missense variant) C/T 0.24 - circulating BC, AC NHS [53]
C/T 0.76 - circulating LUT Healthy French men & women (n=28) [66]
C/T 0.76 + MPOD after 6 mo. LUT supplementation Healthy French men & women (n=28) [66]
C/T 0.24 + circulating BC Healthy UK women (n = 28) [57]
C/T 0.24 - postprandial ROL/BC Healthy UK women (n = 28) [57]
C/T 0.29 - prostate BC after ~25 days tomato juice supplementation American men with prostate cancer (n=47)[60]
rs8044334 upstream T/G 0.24, 0.36, 0.35 + circulating BC inCHIANTI, WHAS, ATBC (placebo arm only)[49]
rs10048138 within G/A 0.14 + circulating LUT+ZEA NHS [53]
G/A 0.31 + post-prandial ROL/BC Healthy UK women (n = 28) [58]
rs11645428 upstream G/A 0.47, 0.33, 0.28 - circulating BC inCHIANTI, WHAS, ATBC (placebo arm only)[49]
G/A 0.33 + MPOD CAREDS postmenopausal women (n=1585) [65]
G/A 0.33 + circulating LUT+ZEA CAREDS postmenopausal women (n=1663) [52]
G/A 0.33 - AMD CAREDS postmenopausal women (n=1663) [52]
G/A 0.29 + post-prandial ROL/BC Healthy UK women (n = 28) [58]
rs129349223 within (missense variant) A/T 0.44 + circulating BC, AC, LUT+ZEA NHS [53]
A/T 0.44 - circulating ROL NHS [53]
A/T 0.44 - circulating BC and LYC after ~25 days of tomato juice supplementation; prostate BC and LYC American men with prostate cancer (n=47)[60]
rs16955008 downstream C/A 0.12 + AMD CAREDS postmenopausal women (n=1663) [52]
rs56389940 downstream C/A 0.36 + circulating LUT+ZEA NHS [53]
1

Location (i.e. upstream, within, or downstream) relative to the coding region of BCO1, and impact on the BCO1 gene (if known), verified via the NIH SNP database (https://www.ncbi.nlm.nih.gov/snp/) utilizing the Genome Reference Consortium Human Build 38 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.39).

2

Effect direction refers to the second allele noted in the previous column.

3

Significant multi-SNP interaction on circulating BC and ROL and breast cancer risk in the population after adjustment for alcohol and pack-years of smoking in NCI BPC population [67]

4

Trend for multi-SNP interaction with provitamin A and vitamin A intakes and CRC risk, after adjustment for age, smoking, alcohol, and NSAIDS in DDCH population [68]