Variant report

Variant	rs11634428
Chromosome Location	chr15:77084582-77084583
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	chr15:77083317..77084988-chr15:77087176..77089675,2	K562	blood:

Extended variants
information (count: 92 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1011083	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs10851888	0.90[CHB][hapmap]
rs10851889	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs10851892	0.83[CEU][hapmap];0.85[CHB][hapmap]
rs11072610	0.90[CHB][hapmap]
rs11072611	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11072612	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs11072613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11072614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11072616	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs11072619	0.83[CEU][hapmap];0.85[CHB][hapmap];0.82[AMR][1000 genomes]
rs11072620	0.82[AMR][1000 genomes]
rs11072625	0.83[CEU][hapmap];0.90[CHB][hapmap];0.88[AMR][1000 genomes]
rs11072626	0.87[CEU][hapmap];0.90[CHB][hapmap];0.82[AMR][1000 genomes]
rs11072628	0.87[AMR][1000 genomes]
rs11072631	0.83[CEU][hapmap];0.90[CHB][hapmap];0.87[AMR][1000 genomes]
rs11072632	0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11072636	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs11072637	0.86[CHB][hapmap]
rs11630185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11631082	0.88[AMR][1000 genomes]
rs11632365	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11632670	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs11632765	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs11633309	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11633869	0.83[CEU][hapmap];0.90[CHB][hapmap];0.82[AMR][1000 genomes]
rs11634266	0.84[CHB][hapmap];0.82[AMR][1000 genomes]
rs11635162	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11636612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11637096	0.90[CHB][hapmap]
rs11637494	0.82[AMR][1000 genomes]
rs11852395	0.90[CHB][hapmap];0.88[AMR][1000 genomes]
rs11855296	0.83[CEU][hapmap];0.83[CHB][hapmap];0.88[AMR][1000 genomes]
rs11855534	0.85[CHB][hapmap]
rs11855644	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12439141	0.83[CEU][hapmap];0.90[CHB][hapmap];0.88[AMR][1000 genomes]
rs12440511	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs12440691	0.82[AMR][1000 genomes]
rs12440965	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs12592686	0.82[AMR][1000 genomes]
rs12898416	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[AMR][1000 genomes]
rs12904149	0.83[CEU][hapmap];0.90[CHB][hapmap];0.88[AMR][1000 genomes]
rs12904417	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs12905181	0.82[AMR][1000 genomes]
rs12913024	0.87[AMR][1000 genomes]
rs12915184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1443115	0.83[CEU][hapmap];0.85[CHB][hapmap];0.88[AMR][1000 genomes]
rs1484990	0.80[CHB][hapmap]
rs1567671	0.83[CEU][hapmap];0.84[CHB][hapmap]
rs2280194	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs2404734	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs28823285	0.85[AMR][1000 genomes]
rs34215663	0.85[AMR][1000 genomes]
rs34998733	0.88[AMR][1000 genomes]
rs35374222	0.88[AMR][1000 genomes]
rs35710279	0.88[AMR][1000 genomes]
rs3764245	0.90[CHB][hapmap]
rs3812908	0.83[CEU][hapmap];0.85[CHB][hapmap]
rs3812909	0.83[CEU][hapmap];0.85[CHB][hapmap]
rs3910756	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4312276	0.83[CEU][hapmap];0.90[CHB][hapmap];0.88[AMR][1000 genomes]
rs4886506	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs4886819	0.90[CHB][hapmap]
rs4886823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886827	0.81[ASN][1000 genomes]
rs4886837	0.83[CEU][hapmap];0.90[CHB][hapmap];0.82[AMR][1000 genomes]
rs55746932	0.82[AMR][1000 genomes]
rs56712156	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs60702982	0.80[AMR][1000 genomes]
rs7165053	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs7178250	0.83[CEU][hapmap];0.90[CHB][hapmap];0.82[AMR][1000 genomes]
rs7181506	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs8025991	0.81[CEU][hapmap];0.89[CHB][hapmap];0.82[AMR][1000 genomes]
rs907593	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs920712	0.82[CEU][hapmap];0.90[CHB][hapmap];0.85[AMR][1000 genomes]
rs9635380	0.83[CEU][hapmap];0.90[CHB][hapmap];0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv904400	chr15:76772062-77085283	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1053924	chr15:76803849-77089079	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv904401	chr15:76816015-77085283	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	esv2830013	chr15:76863023-77176158	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
7	nsv904406	chr15:76869929-77085283	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
8	nsv904407	chr15:76869929-77121196	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
9	nsv904408	chr15:76884127-77085283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1046137	chr15:76892097-77196336	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv542442	chr15:76892097-77196336	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv904411	chr15:76893186-77085283	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv904412	chr15:76910031-77085283	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv457206	chr15:76971456-77121196	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv570110	chr15:76971456-77121196	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11634428	SCAPER	cis	Adipose Subcutaneous	GTEx
rs11634428	SCAPER	cis	Whole Blood	GTEx
rs11634428	ZNF291	cis	lesional skin	skin_eQTL
rs11634428	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs11634428	SCAPER	cis	Thyroid	GTEx
rs11634428	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs11634428	ZNF291	cis	uninvolved skin	skin_eQTL
rs11634428	SCAPER	cis	lung	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77057000-77084600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr15:77057000-77084800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:77057000-77092000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:77057000-77097200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr15:77057200-77098400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr15:77057800-77098200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr15:77058000-77084800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr15:77058000-77084800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr15:77058000-77084800	Weak transcription	Fetal Kidney	kidney
10	chr15:77058000-77085600	Weak transcription	Thymus	Thymus
11	chr15:77058000-77100200	Weak transcription	Fetal Brain Male	brain
12	chr15:77058000-77106000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr15:77058200-77084600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr15:77058200-77084800	Weak transcription	Brain Substantia Nigra	brain
15	chr15:77058200-77085400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr15:77065400-77085200	Weak transcription	Colon Smooth Muscle	Colon
17	chr15:77067200-77084600	Weak transcription	Placenta	Placenta
18	chr15:77067400-77086000	Weak transcription	Brain Angular Gyrus	brain
19	chr15:77069200-77085600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr15:77069600-77085800	Weak transcription	Brain Germinal Matrix	brain
21	chr15:77070000-77093600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:77070000-77097200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:77070200-77085600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:77073000-77084800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr15:77073000-77085400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr15:77073000-77091800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:77073000-77093800	Weak transcription	Gastric	stomach
28	chr15:77073000-77101000	Weak transcription	Lung	lung
29	chr15:77073000-77101400	Weak transcription	Right Ventricle	heart
30	chr15:77073000-77109200	Weak transcription	Spleen	Spleen
31	chr15:77073000-77125000	Weak transcription	Pancreas	Pancrea
32	chr15:77073200-77084600	Weak transcription	Aorta	Aorta
33	chr15:77073200-77085600	Weak transcription	Fetal Stomach	stomach
34	chr15:77073200-77091800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr15:77075000-77084600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:77075800-77092000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr15:77076600-77098000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:77077000-77089000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr15:77078200-77103000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr15:77078600-77087600	Weak transcription	Fetal Intestine Small	intestine
41	chr15:77078600-77091800	Weak transcription	Esophagus	oesophagus
42	chr15:77079600-77097800	Weak transcription	HSMMtube	muscle
43	chr15:77080400-77092000	Weak transcription	HMEC	breast
44	chr15:77082400-77086400	Strong transcription	Primary B cells from cord blood	blood
45	chr15:77082600-77085400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:77082600-77087600	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr15:77082600-77096400	Weak transcription	Colonic Mucosa	Colon
48	chr15:77082800-77087800	Strong transcription	Liver	Liver
49	chr15:77083000-77085200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:77083000-77085800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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