Variant report

Variant	rs12898810
Chromosome Location	chr15:76904738-76904739
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1011083	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1011084	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10152247	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10851888	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851889	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11072597	0.81[AFR][1000 genomes]
rs11072598	0.81[AFR][1000 genomes]
rs11072600	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11072602	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11072607	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072610	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11072612	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072616	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11072618	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11629727	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11630402	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11631082	0.81[EUR][1000 genomes]
rs11631394	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11632670	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11632765	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11635273	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11635463	0.81[AFR][1000 genomes]
rs11637096	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11852777	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854850	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11855762	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11857327	0.81[AFR][1000 genomes]
rs12437981	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12440511	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12440965	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12591622	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12898416	0.81[EUR][1000 genomes]
rs12904149	0.81[EUR][1000 genomes]
rs12904417	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12910081	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12910820	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12914196	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1443115	0.81[EUR][1000 genomes]
rs1603860	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1809875	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047504	0.88[EUR][1000 genomes]
rs2120109	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2164102	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2404604	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2404734	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2436996	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2454450	0.83[EUR][1000 genomes]
rs2454451	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2459361	0.82[EUR][1000 genomes]
rs2469249	0.81[AFR][1000 genomes]
rs28895952	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34103231	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36114653	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886805	0.81[AFR][1000 genomes]
rs4886816	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886819	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56339024	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57682236	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62026889	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62026898	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7165053	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7181506	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8029283	0.93[EUR][1000 genomes]
rs920712	0.80[EUR][1000 genomes]
rs965818	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:47 , 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	nsv471254	chr15:76811390-76978139	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
6	nsv570021	chr15:76813920-76978139	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv570022	chr15:76816015-76978139	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
8	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
9	nsv1042514	chr15:76838221-76906382	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1042089	chr15:76855098-77016127	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1620	chr15:76862152-76914288	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
12	nsv904402	chr15:76863023-76930805	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
13	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
14	nsv1042623	chr15:76863437-76999030	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
15	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
16	nsv904403	chr15:76869929-76951040	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
17	nsv904404	chr15:76869929-77033934	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
18	nsv904405	chr15:76869929-77047915	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
19	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
20	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
21	nsv1048948	chr15:76878362-76910031	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
22	nsv1052133	chr15:76878362-76962756	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
23	nsv116	chr15:76880628-76914288	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
24	esv1815271	chr15:76883346-76930805	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
25	nsv9278	chr15:76884067-76909125	Weak transcription Enhancers ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases
26	nsv570023	chr15:76884127-76978139	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
27	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
28	nsv570045	chr15:76885321-76907376	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases
29	nsv570050	chr15:76885977-76907376	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases
30	nsv570088	chr15:76891342-76907376	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases
31	esv1824106	chr15:76891342-76930805	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
32	nsv1042897	chr15:76891499-76906382	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases
33	nsv1038330	chr15:76891499-76910031	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases
34	nsv1050601	chr15:76891499-76915225	Strong transcription Weak transcription ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
35	nsv1049209	chr15:76891615-76920081	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
36	nsv1046858	chr15:76892097-77020971	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
37	nsv542440	chr15:76892097-77020971	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
38	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
39	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
40	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
41	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
42	nsv904409	chr15:76893186-77033934	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
43	nsv904410	chr15:76893186-77047915	ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
44	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
45	nsv1054164	chr15:76895332-76920081	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
46	nsv1049736	chr15:76895755-76911871	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases
47	nsv1049886	chr15:76902167-76915225	Strong transcription ZNF genes & repeats Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12898810	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs12898810	SCAPER	cis	Muscle Skeletal	GTEx
rs12898810	SCAPER	cis	Artery Tibial	GTEx
rs12898810	SCAPER	cis	Adipose Subcutaneous	GTEx
rs12898810	SCAPER	cis	Thyroid	GTEx
rs12898810	SCAPER	cis	Whole Blood	GTEx
rs12898810	SCAPER	cis	Esophagus Mucosa	GTEx
rs12898810	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs12898810	SCAPER	cis	Nerve Tibial	GTEx
rs12898810	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx
rs12898810	SCAPER	cis	Esophagus Muscularis	GTEx
rs12898810	SCAPER	cis	lung	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76882200-76991400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:76896800-76915600	Weak transcription	Primary B cells from cord blood	blood
3	chr15:76898200-76909600	Weak transcription	Left Ventricle	heart
4	chr15:76898400-76981000	Weak transcription	Pancreas	Pancrea
5	chr15:76901000-76917200	Weak transcription	Gastric	stomach
6	chr15:76902600-76907400	Weak transcription	Fetal Stomach	stomach
7	chr15:76902600-76992000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:76902800-76915600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr15:76902800-76926400	Weak transcription	Dnd41	blood
10	chr15:76903400-76914800	Weak transcription	Small Intestine	intestine
11	chr15:76903400-76940400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr15:76903600-76914000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr15:76904000-76905000	ZNF genes & repeats	Liver	Liver
14	chr15:76904000-76908200	Weak transcription	Primary T cells from cord blood	blood
15	chr15:76904000-76927800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:76904400-76905000	ZNF genes & repeats	Lung	lung
17	chr15:76904400-76905000	ZNF genes & repeats	Ovary	ovary
18	chr15:76904400-76910400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr15:76904400-76923600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr15:76904600-76904800	ZNF genes & repeats	Aorta	Aorta

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