Variant report

Variant	rs3096633
Chromosome Location	chr19:37111817-37111818
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: 111 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10402486	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10407386	0.83[EUR][1000 genomes]
rs11084862	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12610353	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1830031	0.85[EUR][1000 genomes]
rs2033077	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2217081	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2385642	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385643	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3096617	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3096618	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3096619	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3096622	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3096623	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3096627	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3096628	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3096629	0.86[ASN][1000 genomes]
rs3096630	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3096631	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3096632	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3096635	0.85[EUR][1000 genomes]
rs3096636	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108166	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108167	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3108168	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108171	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108172	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3108174	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3108179	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108181	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108182	0.88[EUR][1000 genomes]
rs3108184	0.88[EUR][1000 genomes]
rs3108185	0.88[EUR][1000 genomes]
rs3108186	0.88[EUR][1000 genomes]
rs3108187	0.88[EUR][1000 genomes]
rs3108188	0.88[EUR][1000 genomes]
rs3108189	0.87[EUR][1000 genomes]
rs3108190	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108191	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108192	0.83[EUR][1000 genomes]
rs3108193	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108196	0.80[ASN][1000 genomes]
rs3108197	0.85[EUR][1000 genomes]
rs3108201	0.85[EUR][1000 genomes]
rs3108203	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108205	0.88[EUR][1000 genomes]
rs3108208	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108209	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108214	0.85[EUR][1000 genomes]
rs3108215	0.85[EUR][1000 genomes]
rs3108542	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108543	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108544	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3108545	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108546	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3108549	0.80[ASN][1000 genomes]
rs3108550	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108552	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108555	0.88[EUR][1000 genomes]
rs3108559	0.88[EUR][1000 genomes]
rs3108560	0.88[EUR][1000 genomes]
rs3108562	0.88[EUR][1000 genomes]
rs3108563	0.88[EUR][1000 genomes]
rs3108564	0.88[EUR][1000 genomes]
rs3108565	0.83[EUR][1000 genomes]
rs3108566	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108567	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108568	0.85[EUR][1000 genomes]
rs3108570	0.85[EUR][1000 genomes]
rs3108572	0.85[EUR][1000 genomes]
rs3108574	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108575	0.85[EUR][1000 genomes]
rs3108576	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108577	0.85[EUR][1000 genomes]
rs3108579	0.85[EUR][1000 genomes]
rs3108580	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108592	0.81[ASN][1000 genomes]
rs3108594	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108596	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108597	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108598	0.83[ASN][1000 genomes]
rs3108600	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108602	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108603	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108604	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108607	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3108608	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108609	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108610	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3111541	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3111542	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3111547	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3111549	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3111550	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34002069	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34395293	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4572520	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4806336	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7245414	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7248477	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7252957	0.82[EUR][1000 genomes]
rs7259195	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7259256	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8105197	0.83[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	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
rs3096633	AC092295.7	cis	Esophagus Muscularis	GTEx
rs3096633	ZNF567	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37097000-37112600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr19:37098000-37118200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr19:37098000-37156000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:37098200-37120400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:37101400-37112800	Weak transcription	Osteobl	bone
6	chr19:37102000-37118600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
7	chr19:37102200-37135200	ZNF genes & repeats	Fetal Brain Female	brain
8	chr19:37103000-37118600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
9	chr19:37103600-37112600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:37104400-37114200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
11	chr19:37104400-37118400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
12	chr19:37104400-37125600	ZNF genes & repeats	Brain Germinal Matrix	brain
13	chr19:37105600-37115200	ZNF genes & repeats	Primary B cells from cord blood	blood
14	chr19:37106400-37115400	ZNF genes & repeats	Primary T cells from cord blood	blood
15	chr19:37106800-37114400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
16	chr19:37106800-37151000	ZNF genes & repeats	Adipose Nuclei	Adipose
17	chr19:37106800-37156200	ZNF genes & repeats	Liver	Liver
18	chr19:37107000-37112000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr19:37107000-37112000	ZNF genes & repeats	Left Ventricle	heart
20	chr19:37107000-37114400	ZNF genes & repeats	Colon Smooth Muscle	Colon
21	chr19:37107000-37114600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr19:37107000-37116000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
23	chr19:37107000-37118600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
24	chr19:37107000-37120400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
25	chr19:37107000-37120400	ZNF genes & repeats	Brain Hippocampus Middle	brain
26	chr19:37107000-37125400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr19:37107000-37134800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:37107000-37152400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
29	chr19:37107200-37114400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr19:37107200-37119800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr19:37107400-37117800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
32	chr19:37107400-37118400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr19:37107600-37119600	ZNF genes & repeats	Stomach Smooth Muscle	stomach
34	chr19:37107800-37118400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
35	chr19:37107800-37134600	ZNF genes & repeats	Brain Anterior Caudate	brain
36	chr19:37108000-37115800	ZNF genes & repeats	Fetal Lung	lung
37	chr19:37108200-37114400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
38	chr19:37108200-37114400	ZNF genes & repeats	Brain Substantia Nigra	brain
39	chr19:37108400-37114200	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
40	chr19:37108400-37118400	ZNF genes & repeats	Fetal Muscle Leg	muscle
41	chr19:37108400-37119800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
42	chr19:37108600-37114200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr19:37109000-37112000	ZNF genes & repeats	Fetal Stomach	stomach
44	chr19:37109000-37112600	Weak transcription	Fetal Kidney	kidney
45	chr19:37109200-37119800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
46	chr19:37109200-37120400	ZNF genes & repeats	Dnd41	blood
47	chr19:37109600-37118400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr19:37109800-37114600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr19:37109800-37114600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
50	chr19:37110000-37112600	Weak transcription	Right Ventricle	heart

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