| Literature DB >> 29527544 |
Rector Arya1,2, Agustin Escalante3, Vidya S Farook1,2, Jose F Restrepo3, Daniel F Battafarano4, Marcio Almeida1,2, Mark Z Kos1,2, Marcel J Fourcaudot5, Srinivas Mummidi1,2, Satish Kumar1,2, Joanne E Curran1,2, Christopher P Jenkinson1,2, John Blangero1,2, Ravindranath Duggirala1,2, Inmaculada Del Rincon3.
Abstract
Carotid Intima-media thickness (CIMT) and plaque are well established markers of subclinical atherosclerosis and are widely used for identifying subclinical atherosclerotic disease. We performed association analyses using Metabochip array to identify genetic variants that influence variation in CIMT and plaque, measured using B-mode ultrasonography, in rheumatoid arthritis (RA) patients. Data on genetic associations of common variants associated with both CIMT and plaque in RA subjects involving Mexican Americans (MA) and European Americans (EA) populations are presented in this article. Strong associations were observed after adjusting for covariate effects including baseline clinical characteristics and statin use. Susceptibility loci and genes and/or nearest genes associated with CIMT in MAs and EAs with RA are presented. In addition, common susceptibility loci influencing CIMT and plaque in both MAs and EAs have been presented. Polygenic Risk Score (PRS) plots showing complementary evidence for the observed CIMT and plaque association signals are also shown in this article. For further interpretation and details, please see the research article titled "A Genetic Association Study of Carotid Intima-Media Thickness (CIMT) and Plaque in Mexican Americans and European Americans with Rheumatoid Arthritis" which is being published in Atherosclerosis (Arya et al., 2018) [1].(Arya et al., in press) Thus, common variants in several genes exhibited significant associations with CIMT and plaque in both MAs and EAs as presented in this article. These findings may help understand the genetic architecture of subclinical atherosclerosis in RA populations.Entities:
Year: 2018 PMID: 29527544 PMCID: PMC5842364 DOI: 10.1016/j.dib.2018.02.006
Source DB: PubMed Journal: Data Brief ISSN: 2352-3409
Susceptibility loci associated with carotid IMT in Mexican Americans.
| 6 | rs17526722 | 26,026,834 | I | A | 0.10 | −0.8377 | 0.1797 | 3.80E-06 | |
| 6 | rs36014129 | 25,992,498 | IG | A | 0.10 | −0.85 | 0.184 | 4.63E-06 | |
| 6 | rs13212534 | 26,090,989 | I | A | 0.10 | −0.8607 | 0.1891 | 6.36E-06 | |
| 6 | rs13213957 | 25,894,205 | I | C | 0.10 | −0.7806 | 0.1762 | 1.10E-05 | |
| 6 | rs55912630 | 25,974,914 | I | C | 0.10 | −0.7806 | 0.1762 | 1.10E-05 | |
| 6 | rs13191296 | 25,792,585 | I | T | 0.08 | −0.7771 | 0.176 | 1.19E-05 | |
| 2 | rs4894108 | 180,112,792 | I | G | 0.19 | −0.2501 | 0.05751 | 1.59E-05 | |
| 6 | rs13211947 | 25,972,797 | I | T | 0.10 | −0.8179 | 0.189 | 1.75E-05 | |
| 6 | rs41266779 | 26,129,851 | IG | T | 0.10 | −0.8178 | 0.1891 | 1.78E-05 | |
| 17 | rs2672901 | 76,411,261 | I | A | 0.32 | −0.1929 | 0.04489 | 2.00E-05 | |
| 13 | rs11619113 | 109,716,661 | I | G | 0.20 | −0.3918 | 0.09165 | 2.21E-05 | |
| 13 | rs12873154 | 109,718,853 | I | G | 0.20 | −0.3918 | 0.09165 | 2.21E-05 | |
| 13 | rs11619038 | 109,721,800 | I | T | 0.20 | −0.3918 | 0.09165 | 2.21E-05 | |
| 6 | rs13202688 | 26,101,448 | IG | G | 0.10 | −0.7505 | 0.1762 | 2.37E-05 | |
| 10 | rs61850526 | 63,190,012 | I | T | 0.02 | −0.4624 | 0.1126 | 4.56E-05 | |
| 6 | rs34043431 | 25,983,063 | IG | C | 0.10 | −0.7012 | 0.173 | 5.68E-05 | |
| 11 | rs76599700 | 61,401,283 | I | T | 0.26 | −0.7317 | 0.1814 | 6.17E-05 | |
| 16 | rs11860529 | 82,330,023 | I | T | 0.08 | 0.4112 | 0.1028 | 7.06E-05 | |
| 1 | rs17436982 | 219,622,889 | IG | T | 0.22 | 0.2827 | 0.07173 | 8.98E-05 | |
| 5 | rs250216 | 50,317,115 | IG | C | 0.07 | 0.2322 | 0.05899 | 9.20E-05 | |
| 7 | rs11761467 | 27,828,130 | I | T | 0.10 | −0.3244 | 0.08256 | 9.44E-05 | |
| 13 | rs11620140 | 109,730,512 | I | C | 0.11 | −0.3696 | 0.09417 | 9.62E-05 | |
| 6 | rs11966018 | 12,317,214 | IG | C | 0.03 | 0.691 | 0.1763 | 9.82E-05 | |
| 15 | rs7177074 | 97,357,475 | I | A | 0.05 | −0.5138 | 0.1312 | 9.95E-05 |
Chr. = chromosome; SNP = single nucleotide polymorphism; Loc = Location; I = Intron; IG = Intergenic; MAF = minor allele frequency.
Based on National Center for Biotechnology Information (NCBI) Build36 (hg18).
A1 = minor allele.
p values ranked from low to high.
Susceptibility loci associated with carotid IMT in European Americans.
| 15 | rs1867148 | 73,127,038 | I | C | 0.44 | −0.2804 | 0.06064 | 5.11E-06 | |
| 15 | rs7163636 | 73,133,813 | IG | C | 0.48 | −0.2748 | 0.06053 | 7.51E-06 | |
| 13 | rs323453 | 104,232,379 | IG | G | 0.34 | −0.2724 | 0.06346 | 2.23E-05 | |
| 15 | rs3812945 | 73,076,775 | I | G | 0.45 | 0.2626 | 0.06346 | 2.23E-05 | |
| 1 | rs4846566 | 217,797,888 | IG | T | 0.01 | −1.186 | 0.2777 | 2.46E-05 | |
| 2 | rs12987042 | 38,518,674 | IG | A | 0.36 | −0.2608 | 0.0619 | 3.13E-05 | |
| 1 | rs17006057 | 217,790,022 | IG | A | 0.01 | −1.225 | 0.2915 | 3.29E-05 | |
| 15 | rs6495122 | 72,912,698 | IG | A | 0.42 | −0.2525 | 0.06149 | 4.90E-05 | |
| 1 | rs2645091 | 2,214,505 | I | T | 0.15 | −0.3511 | 0.08741 | 7.07E-05 | |
| 16 | rs17821532 | 52,504,199 | I | A | 0.05 | −0.7006 | 0.1751 | 7.58E-05 | |
| 6 | rs7742814 | 119,185,974 | IG | G | 0.36 | 0.2555 | 0.06462 | 9.09E-05 | |
| 11 | rs4387380 | 5,824,023 | IG | C | 0.03 | −0.8226 | 0.2085 | 9.45E-05 |
Chr. = chromosome; SNP = single nucleotide polymorphism; Loc = Location; I = Intron; IG = Intergenic; MAF = minor allele frequency.
Based on National Center for Biotechnology Information (NCBI) Build36 (hg18).
A1 = minor allele.
p values ranked from low to high.
Common susceptibility loci associated with carotid IMT and plaque in Mexican Americans.
| 6 | rs17526722 | 26,026,834 | I | A | 0.10 | −0.8377 | 0.1797 | 3.80E-06 | 0.04112 | |
| 2 | rs4894108 | 180,112,792 | I | G | 0.19 | −0.2501 | 0.05751 | 1.59E-05 | 0.00823 | |
| 17 | rs2672901 | 76,411,261 | I | A | 0.32 | −0.1929 | 0.04489 | 2.00E-05 | 0.01672 | |
| 13 | rs12873154 | 109,718,853 | I | G | 0.20 | −0.3918 | 0.09165 | 2.21E-05 | 0.04923 | |
| 10 | rs61850526 | 63,190,012 | I | T | 0.02 | −0.4624 | 0.1126 | 4.56E-05 | 0.001367 | |
| 11 | rs76599700 | 61,401,283 | I | T | 0.26 | −0.7317 | 0.1814 | 6.17E-05 | 0.08027 | |
| 16 | rs11860529 | 82,330,023 | I | T | 0.08 | 0.4112 | 0.1028 | 7.06E-05 | 0.02431 | |
| 1 | rs17436982 | 219,622,889 | IG | T | 0.22 | 0.2827 | 0.07173 | 8.98E-05 | 0.006092 | |
| 5 | rs250216 | 50,317,115 | IG | C | 0.07 | 0.2322 | 0.05899 | 9.20E-05 | 0.0262 | |
| 7 | rs11761467 | 27,828,130 | I | T | 0.10 | −0.3244 | 0.08256 | 9.44E-05 | 0.01331 | |
| 6 | rs11966018 | 12,317,214 | IG | C | 0.03 | 0.691 | 0.1763 | 9.82E-05 | 0.009176 | |
| 15 | rs7177074 | 97,357,475 | I | A | 0.05 | −0.5138 | 0.1312 | 9.95E-05 | 0.001647 |
Chr. = chromosome; SNP = single nucleotide polymorphism; Loc = Location; I = Intron; IG = Intergenic; MAF = minor allele frequency.
Based on National Center for Biotechnology Information (NCBI) Build36/130 (hg18).
A1 = minor allele.
p values ranked from low to high.
Common susceptibility loci associated with plaque and CIMT in Mexican Americans.
| 13 | rs496916 | 109,649,015 | I | C | 0.41 | 0.514 | 0.1428 | 3.15E-06 | 0.03256 | |
| 15 | rs9806753 | 46,953,709 | IG | A | 0.26 | 1.739 | 0.1229 | 6.71E-06 | 0.1274 | |
| 6 | rs9463110 | 12,890,588 | I | G | 0.44 | 1.699 | 0.1222 | 1.45E-05 | 0.02229 | |
| 22 | rs2092179 | 38,364,539 | I | C | 0.25 | 0.5883 | 0.1289 | 3.85E-05 | 0.02903 | |
| 9 | rs7869506 | 98,127,033 | I | T | 0.26 | 1.688 | 0.1296 | 5.41E-05 | 0.005388 | |
| 1 | rs6667860 | 36,730,800 | IG | C | 0.48 | 1.658 | 0.1298 | 9.76E-05 | 0.0002729 |
Chr. = chromosome; SNP = single nucleotide polymorphism; Loc = Location; I = Intron; IG = Intergenic; MAF = minor allele frequency.
Based on National Center for Biotechnology Information (NCBI) Build36 (hg18); OR = Odds Ratio.
A1 = minor allele.
p values ranked from low to high.
Common susceptibility loci associated with CIMT and plaque in European Americans.
| Chr. | SNP | Position, bp | Gene/Nearest Gene | Loc. | A1 | MAF | BETA | SE | P | P |
|---|---|---|---|---|---|---|---|---|---|---|
| 15 | rs1867148 | 73,127,038 | I | C | 0.44 | −0.2804 | 0.06064 | 5.11E-06 | 0.01242 | |
| 13 | rs323453 | 104,232,379 | IG | G | 0.34 | −0.2724 | 0.06346 | 2.23E-05 | 0.2049 | |
| 1 | rs4846566 | 217,797,888 | IG | T | 0.01 | −1.186 | 0.2777 | 2.46E-05 | 0.0676 | |
| 2 | rs12987042 | 38,518,674 | IG | A | 0.36 | −0.2608 | 0.0619 | 3.13E-05 | 0.0005153 | |
| 15 | rs6495122 | 72,912,698 | IG | A | 0.42 | −0.2525 | 0.06149 | 4.90E-05 | 0.005717 | |
| 1 | rs2645091 | 2,214,505 | I | T | 0.15 | −0.3511 | 0.08741 | 7.07E-05 | 0.03331 | |
| 16 | rs17821532 | 52,504,199 | I | A | 0.05 | −0.7006 | 0.1751 | 7.58E-05 | 0.03347 | |
| 6 | rs7742814 | 119,185,974 | IG | G | 0.36 | 0.2555 | 0.06462 | 9.09E-05 | 0.3764 | |
| 11 | rs4387380 | 5,824,023 | IG | C | 0.03 | −0.8226 | 0.2085 | 9.45E-05 | 0.06833 |
Chr. = chromosome; SNP = single nucleotide polymorphism; Loc = Location; I = Intron; IG = Intergenic; MAF = minor allele frequency.
Based on National Center for Biotechnology Information (NCBI) Build36 (hg18).
A1 = minor allele.
p values ranked from low to high.
Common susceptibility loci associated with carotid plaque and CIMT in European Americans.
| 12 | rs515291 | 38,689,259 | I | G | 0.32 | 0.4987 | 0.167 | 3.09E-05 | 0.0007138 | |
| 11 | rs10501399 | 68,979,039 | IG | T | 0.09 | 0.2938 | 0.2952 | 3.34E-05 | 0.001367 | |
| 15 | rs692390 | 39,274,282 | I | A | 0.19 | 0.4138 | 0.2157 | 4.30E-05 | 0.0001269 | |
| 5 | rs6887230 | 148,706,339 | I | G | 0.30 | 2.02 | 0.1746 | 5.61E-05 | 0.009851 | |
| 17 | rs2070776 | 59,361,230 | C (ns) | T | 0.33 | 0.5033 | 0.1722 | 6.68E-05 | 0.02914 | |
| 16 | rs3785233 | 7,607,511 | I | C | 0.16 | 0.419 | 0.2229 | 9.49E-05 | 0.0001409 | |
| 6 | rs10948573 | 50,800,310 | I | G | 0.37 | 2.044 | 0.1834 | 9.68E-05 | 0.2071 |
Chr. = chromosome; SNP = single nucleotide polymorphism; Loc = Location; I = Intron; IG = Intergenic; MAF = minor allele frequency.
Based on National Center for Biotechnology Information (NCBI) Build36 (hg18); OR = Odds Ratio.
A1 = minor allele.
p values ranked from low to high.
Fig. 1Q-Q plots for CIMT and plaque association p-values in MAs and EAs.
Fig. 2High-resolution Polygenic Risk Score Model Fit in EA for CIMT (A) and Plaque (B) with theoretical expectations across a range of PT in MA. A. High-resolution Polygenic Risk Score Model Fit in EA for CIMT with theoretical expectations across a range of PT in MA. B. High-resolution Polygenic Risk Score Model Fit in EA for Plaque with theoretical expectations across a range of PT in MA.
| Subject area | |
| More specific subject area | |
| Type of data | |
| How data was acquired | |
| Data format | |
| Experimental factors | |
| Experimental features | |
| Data source location | |
| Data accessibility |