Variant report

Variant	rs3096630
Chromosome Location	chr19:37107097-37107098
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37106532..37109386-chr19:37111281..37113629,2	MCF-7	breast:

Extended variants
information (count: 124 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10402486	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10407386	0.84[EUR][1000 genomes]
rs11084862	0.89[EUR][1000 genomes]
rs11669642	0.82[ASN][1000 genomes]
rs11672680	0.82[ASN][1000 genomes]
rs12610353	0.85[EUR][1000 genomes]
rs1830031	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2033077	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2217081	0.89[EUR][1000 genomes]
rs2385564	0.81[ASN][1000 genomes]
rs2385642	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2385643	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2967453	0.81[ASN][1000 genomes]
rs3096617	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3096618	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3096619	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3096622	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3096623	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3096627	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3096628	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3096629	0.96[ASN][1000 genomes]
rs3096631	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3096632	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3096633	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3096635	0.84[EUR][1000 genomes]
rs3096636	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3108166	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108167	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3108168	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108171	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3108172	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108174	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3108179	0.85[EUR][1000 genomes]
rs3108181	0.89[EUR][1000 genomes]
rs3108182	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3108184	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108185	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108186	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108187	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108188	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108189	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108190	0.89[EUR][1000 genomes]
rs3108191	0.89[EUR][1000 genomes]
rs3108192	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3108193	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108196	0.90[ASN][1000 genomes]
rs3108197	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108201	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108203	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108205	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108206	0.85[AMR][1000 genomes]
rs3108208	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108209	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108214	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108215	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3108218	0.82[ASN][1000 genomes]
rs3108219	0.82[ASN][1000 genomes]
rs3108542	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3108543	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108544	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108545	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108546	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108549	0.90[ASN][1000 genomes]
rs3108550	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108552	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108555	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108559	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108560	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108562	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108563	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108564	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108565	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108566	0.86[EUR][1000 genomes]
rs3108567	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108568	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108570	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108572	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108573	0.82[ASN][1000 genomes]
rs3108574	0.86[EUR][1000 genomes]
rs3108575	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108576	0.86[EUR][1000 genomes]
rs3108577	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108579	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108580	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108583	0.82[ASN][1000 genomes]
rs3108585	0.82[ASN][1000 genomes]
rs3108589	0.82[ASN][1000 genomes]
rs3108590	0.82[ASN][1000 genomes]
rs3108594	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108596	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108597	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108598	0.94[ASN][1000 genomes]
rs3108600	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3108602	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3108603	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3108604	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108607	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3108608	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108609	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108610	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3111541	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3111542	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3111547	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3111549	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3111550	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34002069	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34395293	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4572520	0.95[EUR][1000 genomes]
rs4806336	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62113945	0.81[ASN][1000 genomes]
rs7245414	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7248477	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7250376	0.82[ASN][1000 genomes]
rs7252957	0.83[EUR][1000 genomes]
rs7259195	0.95[EUR][1000 genomes]
rs7259256	0.85[EUR][1000 genomes]
rs8105197	0.83[EUR][1000 genomes];0.80[ASN][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	esv3434386	chr19:37073454-37114509	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3096630	ZNF567	Cis_1M	lymphoblastoid	RTeQTL
rs3096630	AC092295.7	cis	Esophagus Muscularis	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37096800-37110000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:37097000-37107400	Weak transcription	HUVEC	blood vessel
3	chr19:37097000-37107800	Weak transcription	Gastric	stomach
4	chr19:37097000-37112600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:37097200-37109600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr19:37097200-37110000	Weak transcription	NHLF	lung
7	chr19:37098000-37118200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:37098000-37156000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:37098200-37108400	Strong transcription	Brain Inferior Temporal Lobe	brain
10	chr19:37098200-37120400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:37098400-37107400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr19:37098800-37108200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr19:37099000-37109200	Strong transcription	Dnd41	blood
14	chr19:37099200-37110000	Strong transcription	Brain Cingulate Gyrus	brain
15	chr19:37099600-37108400	Strong transcription	Fetal Muscle Leg	muscle
16	chr19:37100200-37107600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr19:37101400-37112800	Weak transcription	Osteobl	bone
18	chr19:37101800-37111000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:37102000-37118600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
20	chr19:37102200-37135200	ZNF genes & repeats	Fetal Brain Female	brain
21	chr19:37103000-37118600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
22	chr19:37103200-37108200	Weak transcription	Brain Substantia Nigra	brain
23	chr19:37103200-37109200	Weak transcription	Right Ventricle	heart
24	chr19:37103600-37107200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:37103600-37112600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:37104000-37107800	Weak transcription	Brain Anterior Caudate	brain
27	chr19:37104200-37107200	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr19:37104400-37114200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
29	chr19:37104400-37118400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
30	chr19:37104400-37125600	ZNF genes & repeats	Brain Germinal Matrix	brain
31	chr19:37105200-37107200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:37105600-37107600	Weak transcription	HepG2	liver
33	chr19:37105600-37110200	Weak transcription	NHDF-Ad	bronchial
34	chr19:37105600-37115200	ZNF genes & repeats	Primary B cells from cord blood	blood
35	chr19:37105800-37107600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr19:37106000-37107400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr19:37106000-37107600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr19:37106200-37107200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
39	chr19:37106200-37109600	Strong transcription	Fetal Heart	heart
40	chr19:37106400-37107200	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
41	chr19:37106400-37108600	Strong transcription	Placenta	Placenta
42	chr19:37106400-37115400	ZNF genes & repeats	Primary T cells from cord blood	blood
43	chr19:37106600-37107800	Weak transcription	Fetal Kidney	kidney
44	chr19:37106800-37107600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr19:37106800-37108200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr19:37106800-37108200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr19:37106800-37110400	ZNF genes & repeats	Fetal Brain Male	brain
48	chr19:37106800-37110800	Strong transcription	HSMMtube	muscle
49	chr19:37106800-37114400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
50	chr19:37106800-37151000	ZNF genes & repeats	Adipose Nuclei	Adipose

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