Variant report

Variant	rs3764245
Chromosome Location	chr15:77223176-77223177
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10851889	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10851892	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11072619	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11072625	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11072626	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11072631	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11072632	0.82[CHB][hapmap]
rs11072636	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072637	0.96[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11633869	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11634266	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11634428	0.90[CHB][hapmap]
rs11635584	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11637296	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11852395	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11855296	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs11855534	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12050866	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12439141	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12898416	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12903331	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12903586	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12904149	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1443115	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1484990	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1567671	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2280194	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2404600	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34450864	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35940181	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3812908	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3812909	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4312276	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4886506	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886837	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4886840	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4886842	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55817928	0.92[ASN][1000 genomes]
rs56275930	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6495224	0.86[ASN][1000 genomes]
rs7178250	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8025991	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs907593	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs907594	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs920712	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9635380	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9707794	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs3764245	SCAPER	cis	Artery Tibial	GTEx
rs3764245	SCAPER	cis	lung	GTEx
rs3764245	SCAPER	cis	Whole Blood	GTEx
rs3764245	SCAPER	cis	Adipose Subcutaneous	GTEx
rs3764245	SCAPER	cis	Nerve Tibial	GTEx
rs3764245	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs3764245	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs3764245	SCAPER	cis	Esophagus Mucosa	GTEx
rs3764245	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx
rs3764245	SCAPER	cis	Thyroid	GTEx
rs3764245	SCAPER	cis	Stomach	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77221200-77223400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:77221600-77223200	Weak transcription	Brain Anterior Caudate	brain
3	chr15:77221600-77223600	Weak transcription	Left Ventricle	heart
4	chr15:77221800-77223200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr15:77222200-77223200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr15:77222200-77223200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr15:77222200-77223400	Enhancers	Fetal Intestine Small	intestine
8	chr15:77222400-77223400	Enhancers	Fetal Intestine Large	intestine
9	chr15:77222800-77223200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:77222800-77223200	Active TSS	HepG2	liver
11	chr15:77223000-77223200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:77223000-77223200	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr15:77223000-77223200	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr15:77223000-77223200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:77223000-77223200	Enhancers	Primary T cells from cord blood	blood
16	chr15:77223000-77223200	Enhancers	Primary hematopoietic stem cells	blood
17	chr15:77223000-77223200	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr15:77223000-77223200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:77223000-77223200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:77223000-77223200	Enhancers	Brain Cingulate Gyrus	brain
21	chr15:77223000-77223200	Enhancers	Brain Hippocampus Middle	brain
22	chr15:77223000-77223200	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr15:77223000-77223200	Enhancers	Brain Substantia Nigra	brain
24	chr15:77223000-77223200	Enhancers	Duodenum Mucosa	Duodenum
25	chr15:77223000-77223200	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr15:77223000-77223200	Enhancers	Fetal Lung	lung
27	chr15:77223000-77223200	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr15:77223000-77223200	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr15:77223000-77223200	Enhancers	Dnd41	blood
30	chr15:77223000-77223200	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr15:77223000-77223200	Enhancers	NHDF-Ad	bronchial
32	chr15:77223000-77223200	Enhancers	NHEK	skin
33	chr15:77223000-77223400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr15:77223000-77223400	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr15:77223000-77223400	Enhancers	Primary B cells from peripheral blood	blood
36	chr15:77223000-77223400	Enhancers	Primary T cells fromperipheralblood	blood
37	chr15:77223000-77223400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr15:77223000-77223400	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr15:77223000-77223400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr15:77223000-77223400	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr15:77223000-77223400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr15:77223000-77223400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:77223000-77223400	Enhancers	Aorta	Aorta
44	chr15:77223000-77223400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr15:77223000-77223600	Flanking Active TSS	A549	lung
46	chr15:77223000-77223600	Flanking Active TSS	K562	blood
47	chr15:77223000-77223800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:77223000-77223800	Flanking Active TSS	Hela-S3	cervix

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