Variant report

Variant	rs12439141
Chromosome Location	chr15:77095423-77095424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr15:77095407-77095805	HEK293-T-REx	kidney:	n/a	chr15:77095545-77095566

Variant related genes	Relation type
SCAPER	TF binding region

Extended variants
information (count: 105 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1011083	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1011084	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10152247	0.82[EUR][1000 genomes]
rs10444809	0.83[ASN][1000 genomes]
rs10851888	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10851889	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10851892	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs11072607	0.80[EUR][1000 genomes]
rs11072610	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs11072611	0.83[CHB][hapmap]
rs11072612	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072613	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs11072614	0.83[CEU][hapmap];0.91[CHB][hapmap]
rs11072616	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072618	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072619	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072620	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072625	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072628	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072631	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11072636	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11072637	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs11629727	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11630185	0.83[CEU][hapmap];0.83[CHB][hapmap]
rs11630402	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11631082	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11631394	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11632365	0.85[AMR][1000 genomes]
rs11632670	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11632765	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11633309	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs11633869	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11634266	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634428	0.83[CEU][hapmap];0.90[CHB][hapmap];0.88[AMR][1000 genomes]
rs11635273	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11636612	0.83[CEU][hapmap];0.83[CHB][hapmap]
rs11637096	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs11637296	0.85[AFR][1000 genomes]
rs11637494	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11852395	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11852777	0.80[EUR][1000 genomes]
rs11855296	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11855534	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11855762	0.80[EUR][1000 genomes]
rs12440511	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12440691	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12440965	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12591622	0.81[EUR][1000 genomes]
rs12592686	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12898416	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12904149	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12904417	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12905181	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12910081	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12910820	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12913024	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12913730	0.86[ASN][1000 genomes]
rs12914196	0.82[EUR][1000 genomes]
rs12915184	0.83[CEU][hapmap];0.83[CHB][hapmap]
rs1443115	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1484990	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1567671	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes]
rs1809875	0.81[EUR][1000 genomes]
rs2137311	0.86[ASN][1000 genomes]
rs2280194	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2404604	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2404734	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs28823285	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34103231	0.81[EUR][1000 genomes]
rs34215663	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34998733	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35374222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35710279	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36114653	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3764245	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3812908	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3812909	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4312276	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886506	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4886819	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4886823	0.83[CEU][hapmap];0.83[CHB][hapmap]
rs4886837	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55746932	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56339024	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60702982	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62026889	0.80[EUR][1000 genomes]
rs62026898	0.82[EUR][1000 genomes]
rs62029232	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7165053	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7178250	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181506	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs8025991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs907593	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs920712	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9635380	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs12439141	SCAPER	cis	Thyroid	GTEx
rs12439141	SCAPER	cis	lung	GTEx
rs12439141	SCAPER	cis	Esophagus Muscularis	GTEx
rs12439141	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx
rs12439141	SCAPER	cis	Artery Tibial	GTEx
rs12439141	SCAPER	cis	Esophagus Mucosa	GTEx
rs12439141	SCAPER	cis	Nerve Tibial	GTEx
rs12439141	SCAPER	cis	Whole Blood	GTEx
rs12439141	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs12439141	SCAPER	cis	Adipose Subcutaneous	GTEx
rs12439141	ZNF291	cis	lesional skin	skin_eQTL
rs12439141	ZNF291	cis	uninvolved skin	skin_eQTL
rs12439141	SCAPER	cis	Muscle Skeletal	GTEx
rs12439141	ISL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77057000-77097200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr15:77057200-77098400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr15:77057800-77098200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr15:77058000-77100200	Weak transcription	Fetal Brain Male	brain
5	chr15:77058000-77106000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr15:77070000-77097200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:77073000-77101000	Weak transcription	Lung	lung
8	chr15:77073000-77101400	Weak transcription	Right Ventricle	heart
9	chr15:77073000-77109200	Weak transcription	Spleen	Spleen
10	chr15:77073000-77125000	Weak transcription	Pancreas	Pancrea
11	chr15:77076600-77098000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:77078200-77103000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr15:77079600-77097800	Weak transcription	HSMMtube	muscle
14	chr15:77082600-77096400	Weak transcription	Colonic Mucosa	Colon
15	chr15:77083600-77097600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:77083800-77095600	Weak transcription	Fetal Lung	lung
17	chr15:77083800-77097800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr15:77083800-77098000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:77084000-77100400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr15:77084000-77100600	Weak transcription	GM12878-XiMat	blood
21	chr15:77084000-77100800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr15:77084400-77098000	Weak transcription	Small Intestine	intestine
23	chr15:77084800-77098200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr15:77085200-77097200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:77085200-77098400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr15:77085400-77096600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr15:77085400-77125000	Weak transcription	HSMM	muscle
28	chr15:77085800-77104400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr15:77086200-77097600	Weak transcription	Hela-S3	cervix
30	chr15:77086200-77097800	Weak transcription	Colon Smooth Muscle	Colon
31	chr15:77086400-77097800	Weak transcription	Brain Germinal Matrix	brain
32	chr15:77086400-77098400	Weak transcription	Brain Substantia Nigra	brain
33	chr15:77086400-77100600	Weak transcription	Aorta	Aorta
34	chr15:77086400-77101600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr15:77086400-77111000	Weak transcription	Thymus	Thymus
36	chr15:77086600-77095600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:77086600-77095600	Weak transcription	Left Ventricle	heart
38	chr15:77087000-77096000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr15:77087200-77098400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr15:77087400-77099200	Weak transcription	Fetal Kidney	kidney
41	chr15:77087600-77097400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:77087600-77098400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr15:77089800-77097800	Weak transcription	Fetal Muscle Leg	muscle
44	chr15:77090600-77096000	Weak transcription	Psoas Muscle	Psoas
45	chr15:77090600-77107800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr15:77091800-77096600	Strong transcription	Primary hematopoietic stem cells	blood
47	chr15:77092000-77097000	Strong transcription	Primary T cells from cord blood	blood
48	chr15:77092200-77097000	Weak transcription	NHEK	skin
49	chr15:77092200-77097200	Weak transcription	A549	lung
50	chr15:77092200-77097600	Weak transcription	K562	blood

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