Skip to main content

Table 3 Enrichment-fold (≥20) of independent LD blocks in the Geuvadis data

From: Prediction of gene expression with cis-SNPs using mixed models and regularization methods

Enrichment fold #Identified SNPs Chromosome LD block
lower upper
26.58 16 2 84,687,169 84,743,579
53.20 11 2 152,118,393 152,146,571
22.76 17 3 19,988,517 20,053,822
184.35 8 3 75,713,481 75,721,542
27.75 17 3 161,090,668 161,144,215
36.70 15 4 44,680,444 44,728,612
81.95 8 4 47,465,736 47,487,305
34.18 13 5 107,006,596 107,052,542
32.41 25 7 120,965,421 121,036,418
299.82 29 10 18,940,551 18,948,334
45.61 12 10 131,909,081 131,934,663
28.64 8 12 127,210,816 127,256,957
44.88 23 12 129,308,528 129,337,972
22.28 17 13 101,241,782 101,327,347
29.80 13 16 5,084,142 5,147,789
23.06 22 18 23,671,164 23,806,409
151.19 16 18 61,616,535 61,637,159
  1. We obtained a total of 18,896 complete records (mainly including the information of disease/trait, chromosome id and position) of identified SNPs by GWASs from https://www.genome.gov/gwastudies/. We counted the number (given in the second column) of related SNPs within 1 Mb upstream and downstream regions near each LD block. These identified SNPs are extensively related to about 130 different types of complex diseases and traits. For example, in the first LD block (Chr2: 84,687,169-84,743,579), previous GWASs have discovered 16 associated SNPs, which, in terms of the catalog of published GWASs, are related to aging traits, protein quantitative trait loci, pulmonary function decline, IgG glycosylation, RR interval heart rate, the response to antipsychotic therapy, coronary artery calcification, prostate cancer, response to cytadine analogues cytosine arabinoside, bilirubin levels, orthostatic hypotension, breast cancer and conduct disorder