Variant report

Variant	rs3812909
Chromosome Location	chr15:77176200-77176201
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 15 )

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

rs_ID	r²[population]
rs1011083	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs10851889	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10851892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072616	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs11072619	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs11072625	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11072626	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11072631	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11072636	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072637	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11633869	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs11634266	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11634428	0.83[CEU][hapmap];0.85[CHB][hapmap]
rs11635584	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11637296	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11852395	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11855296	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs11855534	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12050866	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12439141	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12440511	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12898416	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12903331	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12903586	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12904149	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12909065	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1443115	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1484990	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1567671	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2280194	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2404600	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34450864	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35940181	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3764245	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3812908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4312276	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4886506	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886837	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs4886840	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886842	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55817928	0.84[ASN][1000 genomes]
rs56275930	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495224	0.86[ASN][1000 genomes]
rs7165053	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7178250	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs8025991	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs907593	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs907594	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs920712	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9635380	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9707794	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	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
4	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
5	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
6	esv1803942	chr15:77151005-77210457	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	esv2758388	chr15:77170550-77373448	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	esv2760041	chr15:77170550-77373448	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs3812909	SCAPER	cis	Stomach	GTEx
rs3812909	SCAPER	cis	Esophagus Mucosa	GTEx
rs3812909	ZNF291	cis	uninvolved skin	skin_eQTL
rs3812909	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs3812909	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs3812909	SCAPER	cis	Esophagus Muscularis	GTEx
rs3812909	SCAPER	cis	lung	GTEx
rs3812909	SCAPER	cis	Artery Tibial	GTEx
rs3812909	ZNF291	cis	lesional skin	skin_eQTL
rs3812909	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx
rs3812909	SCAPER	cis	Thyroid	GTEx
rs3812909	ISL2	cis	Whole Blood	GTEx
rs3812909	SCAPER	cis	Adipose Subcutaneous	GTEx
rs3812909	SCAPER	cis	Nerve Tibial	GTEx
rs3812909	SCAPER	cis	Whole Blood	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77112200-77196000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr15:77133200-77196800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr15:77140800-77195800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr15:77142000-77195800	Weak transcription	Right Ventricle	heart
5	chr15:77144800-77179000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr15:77146400-77196400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:77147800-77177200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr15:77148600-77195600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr15:77148800-77181000	Weak transcription	Fetal Kidney	kidney
10	chr15:77148800-77195600	Weak transcription	Dnd41	blood
11	chr15:77154400-77179600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr15:77156400-77176400	Weak transcription	Psoas Muscle	Psoas
13	chr15:77158600-77179800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:77158600-77180600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr15:77158600-77190800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr15:77158800-77177800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:77158800-77195600	Weak transcription	Brain Hippocampus Middle	brain
18	chr15:77158800-77195600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr15:77159400-77176800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr15:77161400-77188800	Weak transcription	Fetal Heart	heart
21	chr15:77166800-77177800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr15:77167600-77177200	Weak transcription	Hela-S3	cervix
23	chr15:77168000-77179600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr15:77168000-77179600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:77168200-77177400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr15:77168400-77179400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:77168400-77195000	Weak transcription	Adipose Nuclei	Adipose
28	chr15:77168600-77177200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr15:77168600-77178000	Weak transcription	Gastric	stomach
30	chr15:77168600-77179600	Weak transcription	Lung	lung
31	chr15:77168600-77180000	Weak transcription	Esophagus	oesophagus
32	chr15:77168600-77180800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:77168600-77181600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:77168600-77195000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:77168600-77195600	Weak transcription	Colon Smooth Muscle	Colon
36	chr15:77168600-77196800	Weak transcription	Pancreas	Pancrea
37	chr15:77168600-77196800	Weak transcription	Spleen	Spleen
38	chr15:77168800-77179200	Weak transcription	Fetal Brain Female	brain
39	chr15:77169400-77179200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr15:77170200-77190600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:77171800-77176200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr15:77172000-77179200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr15:77172200-77182400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr15:77172400-77176400	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr15:77172800-77195600	Weak transcription	HSMM	muscle
46	chr15:77173200-77176200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr15:77173400-77178400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr15:77173400-77179200	Weak transcription	HepG2	liver
49	chr15:77173600-77179800	Weak transcription	Brain Substantia Nigra	brain
50	chr15:77173800-77183600	Weak transcription	Primary T cells from cord blood	blood

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