Variant report

Variant	rs7585590
Chromosome Location	chr2:20427191-20427192
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:20421499..20423791-chr2:20425335..20427623,2	K562	blood:

Variant related genes	Relation type
ENSG00000115884	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10175853	0.92[CEU][hapmap]
rs10192042	0.92[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs1043400	0.95[MEX][hapmap]
rs10495704	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1106111	0.93[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.94[ASN][1000 genomes]
rs11096648	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11096649	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11096650	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11888357	0.90[MEX][hapmap]
rs11895228	0.83[CEU][hapmap]
rs11896241	0.85[MEX][hapmap]
rs12373772	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12373819	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12464428	0.93[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs12472685	0.81[EUR][1000 genomes]
rs13415389	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2002090	0.93[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.94[ASN][1000 genomes]
rs2007340	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2110410	0.81[MEX][hapmap]
rs34678899	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3732162	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732163	0.89[ASN][1000 genomes]
rs3732164	0.89[ASN][1000 genomes]
rs3755300	0.91[ASN][1000 genomes]
rs3771227	0.85[ASN][1000 genomes]
rs3771229	0.94[ASN][1000 genomes]
rs3771232	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3771233	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3771236	0.85[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs3771238	0.81[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs3771239	0.86[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs3771240	0.96[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3771241	0.89[ASN][1000 genomes]
rs3771243	0.93[ASN][1000 genomes]
rs3771244	0.89[ASN][1000 genomes]
rs3771246	0.89[ASN][1000 genomes]
rs3771247	0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs3821218	0.85[MEX][hapmap]
rs3821219	0.90[ASN][1000 genomes]
rs57938873	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59129757	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62109740	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62111433	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62123442	0.81[EUR][1000 genomes]
rs6748274	0.85[MEX][hapmap]
rs72785203	0.94[ASN][1000 genomes]
rs72785204	0.94[ASN][1000 genomes]
rs72785206	0.94[ASN][1000 genomes]
rs7558833	0.91[CEU][hapmap];0.89[GIH][hapmap];0.82[TSI][hapmap]
rs7563245	0.96[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9306890	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1798036	chr2:20423264-20442631	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv1846193	chr2:20423264-20442631	Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv1849406	chr2:20423264-20442631	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv1819683	chr2:20423264-20455467	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7585590	GEN1	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20425600-20427800	Weak transcription	Osteobl	bone
2	chr2:20425600-20429400	Weak transcription	NHDF-Ad	bronchial
3	chr2:20425600-20429800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:20425800-20427800	Enhancers	HMEC	breast
5	chr2:20425800-20431000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:20425800-20431000	Weak transcription	NH-A	brain
7	chr2:20426000-20427600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:20426000-20430600	Weak transcription	Hela-S3	cervix
9	chr2:20426000-20447000	Weak transcription	GM12878-XiMat	blood
10	chr2:20426200-20427400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:20426200-20427400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:20426200-20427600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:20426200-20431000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:20426200-20431000	Weak transcription	Colonic Mucosa	Colon
15	chr2:20426200-20431000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr2:20426200-20431000	Weak transcription	A549	lung
17	chr2:20426200-20431200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr2:20426200-20431200	Weak transcription	Gastric	stomach
19	chr2:20426200-20436600	Weak transcription	Pancreas	Pancrea
20	chr2:20426400-20430400	Weak transcription	NHEK	skin
21	chr2:20426400-20430600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:20426400-20430800	Weak transcription	Esophagus	oesophagus
23	chr2:20426400-20430800	Weak transcription	HepG2	liver
24	chr2:20426400-20431000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:20426400-20431000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:20426400-20431000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:20426400-20431200	Weak transcription	Fetal Intestine Large	intestine
28	chr2:20426400-20436800	Enhancers	Placenta	Placenta
29	chr2:20426600-20431000	Weak transcription	Rectal Mucosa Donor 29	rectum

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