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

BMC Genomics

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

Enrichment fold	#Identified SNPs	Chromosome	LD block
Enrichment fold	#Identified SNPs	Chromosome	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

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

ISSN: 1471-2164