Variant report

Variant	rs1484990
Chromosome Location	chr15:77055335-77055336
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77052021..77055015-chr15:77055082..77056903,3	K562	blood:

Extended variants
information (count: 99 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1011083	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1011084	0.81[ASN][1000 genomes]
rs10444809	0.89[ASN][1000 genomes]
rs10851888	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10851889	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10851892	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11072610	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11072612	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs11072614	0.86[CHB][hapmap]
rs11072616	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11072618	0.81[ASN][1000 genomes]
rs11072619	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11072620	0.91[ASN][1000 genomes]
rs11072625	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11072626	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11072628	0.86[ASN][1000 genomes]
rs11072631	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11072636	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11072637	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11629727	0.81[ASN][1000 genomes]
rs11631082	0.91[ASN][1000 genomes]
rs11631394	0.81[ASN][1000 genomes]
rs11632670	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11632765	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11633869	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11634266	0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11634428	0.80[CHB][hapmap]
rs11635273	0.81[ASN][1000 genomes]
rs11637096	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11637494	0.83[ASN][1000 genomes]
rs11852395	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs11855296	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11855534	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12439141	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12440511	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12440691	0.84[ASN][1000 genomes]
rs12440965	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12592686	0.83[ASN][1000 genomes]
rs12898416	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12904149	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12904417	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12905181	0.86[ASN][1000 genomes]
rs12910081	0.83[ASN][1000 genomes]
rs12910820	0.81[ASN][1000 genomes]
rs12913024	0.85[ASN][1000 genomes]
rs12913730	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1443115	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1567671	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2047504	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2137311	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2280194	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2404604	0.81[ASN][1000 genomes]
rs2404734	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2454451	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs28823285	0.92[ASN][1000 genomes]
rs34215663	0.89[ASN][1000 genomes]
rs34998733	0.88[ASN][1000 genomes]
rs35374222	0.89[ASN][1000 genomes]
rs35710279	0.88[ASN][1000 genomes]
rs36114653	0.84[ASN][1000 genomes]
rs3764245	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3812908	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs3812909	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4312276	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4886506	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4886816	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4886819	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4886837	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs55746932	0.89[ASN][1000 genomes]
rs56339024	0.81[ASN][1000 genomes]
rs60702982	0.87[ASN][1000 genomes]
rs7165053	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7178250	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7181506	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs8025991	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs8037847	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs907593	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs920712	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9635380	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs965818	0.91[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 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	nsv1039269	chr15:76863437-77057021	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	nsv1043066	chr15:76892097-77057021	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv542441	chr15:76892097-77057021	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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
16	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
17	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
18	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
19	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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1484990	SCAPER	cis	Artery Tibial	GTEx
rs1484990	ZNF291	cis	lesional skin	skin_eQTL
rs1484990	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs1484990	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs1484990	ISL2	cis	Whole Blood	GTEx
rs1484990	ZNF291	cis	uninvolved skin	skin_eQTL
rs1484990	SCAPER	cis	Whole Blood	GTEx
rs1484990	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx
rs1484990	SCAPER	cis	Adipose Subcutaneous	GTEx
rs1484990	SCAPER	cis	lung	GTEx
rs1484990	SCAPER	cis	Thyroid	GTEx
rs1484990	SCAPER	cis	Esophagus Mucosa	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76989600-77055800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr15:76992400-77056200	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:76992400-77056200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr15:76992800-77056000	Weak transcription	Right Ventricle	heart
5	chr15:76993200-77056200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:76994200-77056000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr15:77012800-77056200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr15:77016600-77056000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr15:77021000-77055800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:77021000-77056000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr15:77023200-77056000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr15:77023400-77056000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:77023600-77056400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:77025200-77056400	Weak transcription	Hela-S3	cervix
15	chr15:77025400-77056400	Weak transcription	Esophagus	oesophagus
16	chr15:77025600-77055400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr15:77025600-77056000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:77025600-77056400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:77025600-77056400	Weak transcription	Gastric	stomach
20	chr15:77025600-77056400	Weak transcription	Lung	lung
21	chr15:77025600-77056400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr15:77025800-77056000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr15:77025800-77056200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr15:77030200-77055400	Weak transcription	Fetal Kidney	kidney
25	chr15:77030800-77056400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr15:77031000-77056200	Weak transcription	Fetal Stomach	stomach
27	chr15:77031800-77056000	Weak transcription	Brain Substantia Nigra	brain
28	chr15:77032400-77056400	Weak transcription	Left Ventricle	heart
29	chr15:77032600-77056000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr15:77034200-77056000	Weak transcription	Fetal Heart	heart
31	chr15:77034400-77056200	Weak transcription	Small Intestine	intestine
32	chr15:77036400-77056200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr15:77036400-77056400	Weak transcription	Psoas Muscle	Psoas
34	chr15:77037600-77055600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr15:77039000-77056000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr15:77039600-77055400	Weak transcription	Primary B cells from cord blood	blood
37	chr15:77040200-77056000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr15:77040200-77056200	Weak transcription	Brain Anterior Caudate	brain
39	chr15:77040200-77056400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr15:77040200-77056400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:77040200-77056400	Weak transcription	Aorta	Aorta
42	chr15:77040200-77056400	Weak transcription	Pancreas	Pancrea
43	chr15:77040200-77056400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr15:77040200-77056400	Weak transcription	Spleen	Spleen
45	chr15:77040400-77056000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr15:77040400-77056200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:77040400-77056400	Weak transcription	Thymus	Thymus
48	chr15:77043600-77056000	Weak transcription	HSMM	muscle
49	chr15:77046200-77056000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:77046800-77067800	Weak transcription	HUVEC	blood vessel

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