Variant report

Variant	rs3096619
Chromosome Location	chr19:37067060-37067061
allele	A/C
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	CTCF	chr19:37066940-37067090	GM12866	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:37063014..37065659-chr19:37066533..37068326,2	MCF-7	breast:
2	chr19:37018040..37020429-chr19:37065746..37067402,2	K562	blood:
3	chr19:37062757..37067111-chr19:37067178..37071986,8	K562	blood:
4	chr19:37065150..37067798-chr19:37072514..37074047,2	K562	blood:

Variant related genes	Relation type
ENSG00000233527	TF binding region
ZNF529	TF binding region
ENSG00000233527	Chromatin interaction
ENSG00000228629	Chromatin interaction
ENSG00000186020	Chromatin interaction
ENSG00000254004	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10402486	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10407386	0.83[EUR][1000 genomes]
rs11084862	0.88[EUR][1000 genomes]
rs12610353	0.84[EUR][1000 genomes]
rs1830031	0.91[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2033077	0.91[CHB][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2217081	0.88[EUR][1000 genomes]
rs2385642	0.91[JPT][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2385643	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2967453	0.86[ASN][1000 genomes]
rs3096617	0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3096618	0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3096622	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3096623	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3096627	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3096628	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3096629	0.96[ASN][1000 genomes]
rs3096630	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3096631	0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3096632	0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3096633	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3096635	0.83[EUR][1000 genomes]
rs3096636	0.91[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108166	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108167	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108168	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108171	0.84[CHB][hapmap];0.81[JPT][hapmap];0.97[EUR][1000 genomes]
rs3108172	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108174	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108179	0.84[EUR][1000 genomes]
rs3108181	0.84[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes]
rs3108182	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3108184	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108185	0.92[CHB][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108186	0.92[CHB][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108187	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108188	0.92[CHB][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108189	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108190	0.88[EUR][1000 genomes]
rs3108191	0.84[CHB][hapmap];0.88[EUR][1000 genomes]
rs3108192	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3108193	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108196	0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap];0.85[ASN][1000 genomes]
rs3108197	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3108201	1.00[CHB][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3108203	0.92[CHB][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108205	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108206	0.81[AMR][1000 genomes]
rs3108208	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108209	0.92[CHB][hapmap];0.81[JPT][hapmap];0.94[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108214	0.91[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs3108215	0.92[CHB][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3108542	0.95[EUR][1000 genomes]
rs3108543	0.84[CHB][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap];0.95[EUR][1000 genomes]
rs3108544	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108545	0.91[CHB][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108546	0.91[CHB][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108549	0.91[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs3108550	0.91[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108552	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108555	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108559	0.91[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108560	0.92[CHB][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108562	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108563	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3108564	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108565	0.83[EUR][1000 genomes]
rs3108566	0.85[EUR][1000 genomes]
rs3108567	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108568	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3108570	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3108572	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3108574	0.85[EUR][1000 genomes]
rs3108575	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3108576	0.85[EUR][1000 genomes]
rs3108577	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3108579	0.85[EUR][1000 genomes]
rs3108580	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108596	0.92[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108597	0.92[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108598	0.91[CHB][hapmap];0.91[JPT][hapmap];0.99[ASN][1000 genomes]
rs3108600	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3108602	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3108603	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3108604	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108607	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108608	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108609	0.84[CHB][hapmap];0.81[JPT][hapmap];0.96[EUR][1000 genomes]
rs3108610	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3111541	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3111542	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3111547	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3111549	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3111550	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34002069	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34395293	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4572520	0.94[EUR][1000 genomes]
rs4806336	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4806351	0.86[YRI][hapmap]
rs62113945	0.86[ASN][1000 genomes]
rs7245414	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7248477	0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7252957	0.82[EUR][1000 genomes]
rs7259195	0.94[EUR][1000 genomes]
rs7259256	0.84[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs8105197	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
7	esv3334779	chr19:37050161-37076919	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3096619	AC092295.7	cis	Esophagus Muscularis	GTEx
rs3096619	ZNF567	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37064600-37068800	ZNF genes & repeats	A549	lung
2	chr19:37065200-37067200	Weak transcription	Aorta	Aorta
3	chr19:37065200-37068000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:37065200-37068000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr19:37065400-37067800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr19:37065400-37068000	Weak transcription	Gastric	stomach
7	chr19:37065400-37068000	Weak transcription	Left Ventricle	heart
8	chr19:37065600-37067200	Weak transcription	HSMM	muscle
9	chr19:37065600-37067600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr19:37065600-37067600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr19:37065600-37067800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr19:37065600-37067800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:37065600-37067800	Weak transcription	Primary B cells from cord blood	blood
14	chr19:37065600-37067800	Weak transcription	Colonic Mucosa	Colon
15	chr19:37065600-37067800	Weak transcription	Esophagus	oesophagus
16	chr19:37065600-37067800	Weak transcription	Ovary	ovary
17	chr19:37065600-37067800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr19:37065600-37068000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr19:37065600-37068000	Weak transcription	Brain Germinal Matrix	brain
20	chr19:37065600-37068000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr19:37065600-37068000	Weak transcription	Lung	lung
22	chr19:37065600-37068000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr19:37065600-37068000	Weak transcription	Spleen	Spleen
24	chr19:37065600-37068200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr19:37065600-37068600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr19:37065600-37069600	Weak transcription	Psoas Muscle	Psoas
27	chr19:37065600-37070200	Weak transcription	HSMMtube	muscle
28	chr19:37065600-37070200	Weak transcription	NHLF	lung
29	chr19:37065600-37081200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr19:37065600-37095400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr19:37065800-37067200	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr19:37065800-37067200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr19:37065800-37067400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr19:37065800-37067800	Weak transcription	Brain Hippocampus Middle	brain
35	chr19:37065800-37067800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr19:37065800-37067800	Weak transcription	NHDF-Ad	bronchial
37	chr19:37065800-37067800	Weak transcription	NHEK	skin
38	chr19:37065800-37068000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr19:37065800-37068000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr19:37065800-37068000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:37065800-37068400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr19:37065800-37068400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr19:37065800-37068400	Weak transcription	Right Atrium	heart
44	chr19:37065800-37069400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr19:37065800-37070000	Weak transcription	Brain Angular Gyrus	brain
46	chr19:37065800-37071200	Weak transcription	Brain Substantia Nigra	brain
47	chr19:37065800-37072000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr19:37065800-37072600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr19:37065800-37075200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:37065800-37076600	Weak transcription	Stomach Mucosa	stomach

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