Research ArticleGENETICS

Genome-wide association study in almost 195,000 individuals identifies 50 previously unidentified genetic loci for eye color

See allHide authors and affiliations

Science Advances  10 Mar 2021:
Vol. 7, no. 11, eabd1239
DOI: 10.1126/sciadv.abd1239
  • Table 1 Strongest associated SNPs from the 52 genomic regions independently associated with eye color in the European discovery cohort (N = 157,485).

    A full list of 115 independently associated SNPs from conditional analysis at these loci can be found in table ST1. SNPs with novel associations for eye color identified here are highlighted in bold. SNPs that were associated with other pigmentation traits, but not iris color, in previous studies are indicated by an asterisk (*). Chr is the chromosome for the given SNP, genome position (Pos) refer to the HG build 37, RS is the rsid for the given SNP, Freq is the allele frequency of the stated reference allele, Beta is the effect size for the stated reference allele, SE is the respective standard error for the beta, Alt allele is the alternative allele for the given SNP, and N is the sample size tested for the respective SNP.

    RegionChrPosRSNearest geneRef alleleAlt alleleNFreqBetaSEP
    119166344rs6693258GPR157TC1574830.216−0.0560.00919.86 × 10−10
    2142110888rs6696511HIVEP3TC1574830.3820.1090.00771.35 × 10−45
    31212421629rs351385*DTLGA1574830.580−0.0830.00752.31 × 10−28
    41236035805rs2385028LYSTTC1574830.2450.0610.00862.43 × 10−12
    5246233381rs13016869PRKCEGC1574830.208−0.0580.00922.23 × 10−10
    62206950236rs112747614INO80DGC1574830.6960.0540.00813.69 × 10−11
    72219755011rs121908120WNT10ATA1574830.9760.1400.02471.54 × 10−8
    82223483670rs12614022FARSBGA1574830.6360.0480.00784.26 × 10−10
    92239276278rs74409360TRAF3IP1TC1574830.076−0.1280.01408.09 × 10−20
    10342762488rs3912104CCDC13TA1574830.5410.0450.00751.47 × 10−9
    11369980177rs116359091*MITFGA1574830.974−0.2290.02461.02 × 10−20
    12423939399rs4521336PPARGC1ATC1574830.3590.0480.00791.28 × 10−9
    13459359559rs141318671No geneGA1574830.993−0.3180.05682.09 × 10−8
    14490059434rs6828137TIGD2TG1574830.457−0.0410.00753.93 × 10−8
    155311902rs62330021PDCD6, AHRRGA1574830.948−0.3250.01711.36 × 10−80
    16533951693rs16891982*SLC45A2GC1574830.958−0.6540.01911.97 × 10−255
    17540273518rs348613DAB2GA1574830.0010.7310.12272.54 × 10−9
    185123896988rs72777200ZNF608TC1574830.8280.0740.01001.22 × 10−13
    195148216187rs11957757ADRB2GA1574830.5470.0420.00752.94 × 10−8
    206396321rs12203592*IRF4TC1574830.171−0.3850.01001.61 × 10−321
    21610538183rs6910861GCNT2GA1574830.4610.0780.00761.20 × 10−24
    226158841725rs341147TULP4GA1574830.343−0.0450.00786.45 × 10−9
    23745960645rs2854746IGFBP3GC1574830.587−0.0430.00761.24 × 10−8
    24783653553rs6944702SEMA3ATC1574830.5120.0480.00751.71 × 10−10
    25812690997rs6997494LONRF1TG1574830.4800.0480.00741.07 × 10−10
    26842003663rs12543326*AP3M2GA1574830.8750.0650.01139.07 × 10−9
    27881350433rs147068120ZBTB10TC1574830.038−0.1220.01988.34 × 10−10
    28912677471rs13297008*TYRP1GA1574830.3880.2600.00774.99 × 10−250
    29927366436rs12552712MOB3BTC1574830.604−0.0560.00772.79 × 10−13
    309132001056rs12335410IER5LTC1574830.221−0.0580.00901.28 × 10−10
    311168831364rs72928978*TPCN2GA1574830.8770.1420.01216.42 × 10−32
    321189017961rs1126809*TYRGA1574830.7210.2850.00831.82 × 10−255
    331223979791rs9971729*SOX5CA1574830.5660.0820.00765.03 × 10−27
    341292567833rs790464BTG1TC1574830.1890.0600.00964.50 × 10−10
    351374178399rs2095645KLF12GA1574830.6720.0500.00793.26 × 10−10
    361395189401rs9301973*DCTGA1574830.6710.0660.00801.48 × 10−16
    371469236136rs138777265ZFP36L1CA1574830.047−0.1090.01766.21 × 10−10
    381492780387rs17184180*SLC24A4TA1574830.5670.2710.00751.34 × 10−284
    391528211758rs4778218*OCA2GA1574830.834−0.5200.0100<1 × 10−330
    401528356859rs1129038*HERC2TC1574830.734−2.6050.0058<1 × 10−330
    411548426484rs1426654SLC24A5GA1574830.1020.6840.06442.72 × 10−26
    42161376386rs761063UBE2IGC1574830.277−0.0500.00842.07 × 10−9
    43171966889rs4790309SMG6TC1574830.4560.0410.00753.71 × 10−8
    441767497367rs3809761MAP2K6GA1574830.8110.0590.01015.08 × 10−9
    451779612397rs6420484*TSPAN10GA1574830.645−0.1610.00807.53 × 10−90
    46197581625rs73488486ZNF358TG1574830.0970.0860.01282.40 × 10−11
    47204948248rs2748901SLC23A2GA1574830.463−0.0470.00753.37 × 10−10
    482138568882rs2835660TTC3GC1574830.545−0.0640.00751.62 × 10−17
    492144783287rs622330*SIK1GA1574830.5120.1110.00753.87 × 10−49
    502246369657rs35051352WNT7BGC1478750.549−0.0620.00813.33 × 10−14
    512348118832rs78542430SSX1TA1574830.450−0.0950.00625.93 × 10−53
    5223119439335rs5957354TMEM255ATA1574830.861−0.0900.00925.43 × 10−23

Supplementary Materials

  • Supplementary Materials

    Genome-wide association study in almost 195,000 individuals identifies 50 previously unidentified genetic loci for eye color

    Mark Simcoe, Ana Valdes, Fan Liu, Nicholas A. Furlotte, David M. Evans, Gibran Hemani, Susan M. Ring, George Davey Smith, David L. Duffy, Gu Zhu, Scott D. Gordon, Sarah E. Medland, Dragana Vuckovic, Giorgia Girotto, Cinzia Sala, Eulalia Catamo, Maria Pina Concas, Marco Brumat, Paolo Gasparini, Daniela Toniolo, Massimiliano Cocca, Antonietta Robino, Seyhan Yazar, Alex Hewitt, Wenting Wu, Peter Kraft, Christopher J. Hammond, Yuan Shi, Yan Chen, Changqing Zeng, Caroline C. W. Klaver, Andre G. Uitterlinden, M. Arfan Ikram, Merel A. Hamer, Cornelia M. van Duijn, Tamar Nijsten, Jiali Han, David A. Mackey, Nicholas G. Martin, Ching-Yu Cheng, the 23andMe Research Team, the International Visible Trait Genetics Consortium, David A. Hinds, Timothy D. Spector, Manfred Kayser, Pirro G. Hysi

    Download Supplement

    The PDF file includes:

    • Sections S1 to S3
    • Legends for tables S1 to S9
    • Figs. S1 and S2
    • Legends for Supplementary Author Files 1 and 2
    • References

    Other Supplementary Material for this manuscript includes the following:

    Files in this Data Supplement:

Stay Connected to Science Advances

Navigate This Article