Variant report

Variant	rs797866
Chromosome Location	chr3:101658031-101658032
allele	C/T
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	GATA3	chr3:101657942-101660957	SK-N-SH	brain:	n/a	chr3:101659283-101659299 chr3:101659288-101659299 chr3:101659281-101659302 chr3:101659579-101659589 chr3:101659930-101659938 chr3:101659288-101659295 chr3:101659288-101659295 chr3:101659288-101659295 chr3:101659286-101659295 chr3:101659286-101659296
2	NFIC	chr3:101657980-101660977	SK-N-SH	brain:	n/a	chr3:101659513-101659530

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:101655492..101658302-chr3:101660937..101663877,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214407	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10470501	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1081574	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1081576	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1088047	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1091320	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1091664	0.90[ASN][1000 genomes]
rs1378838	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1513118	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1626282	0.84[AFR][1000 genomes]
rs1672380	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1672386	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1707608	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1707613	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1707618	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1707619	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28542140	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2860329	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2925323	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2925325	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2925326	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2942716	0.82[AFR][1000 genomes]
rs2951443	0.90[AFR][1000 genomes]
rs654102	0.87[ASN][1000 genomes]
rs675779	1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs771324	0.83[ASN][1000 genomes]
rs771573	0.90[ASN][1000 genomes]
rs771574	0.90[ASN][1000 genomes]
rs771575	0.90[ASN][1000 genomes]
rs9869373	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9881690	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv3351469	chr3:101511702-101866448	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1010762	chr3:101584836-101803821	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101643800-101658400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:101653200-101659200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr3:101654000-101659200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:101654000-101659200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:101654000-101660200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr3:101654000-101661400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:101654000-101662800	Enhancers	Primary B cells from peripheral blood	blood
8	chr3:101654200-101659000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr3:101654200-101659400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr3:101654200-101662200	Enhancers	Primary T cells from cord blood	blood
11	chr3:101654400-101659200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:101655000-101658600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:101655000-101658600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:101655400-101659000	Enhancers	HUVEC	blood vessel
15	chr3:101655400-101659600	Weak transcription	Fetal Thymus	thymus
16	chr3:101655400-101660000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:101655600-101659400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:101655600-101660000	Enhancers	Hela-S3	cervix
19	chr3:101655600-101660600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:101655800-101659400	Enhancers	HSMMtube	muscle
21	chr3:101656000-101658600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:101656000-101658600	Enhancers	HSMM	muscle
23	chr3:101656000-101658800	Enhancers	NHDF-Ad	bronchial
24	chr3:101656000-101659200	Enhancers	Osteobl	bone
25	chr3:101656000-101659400	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr3:101656000-101659600	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr3:101656000-101659600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr3:101656000-101661400	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr3:101656000-101661600	Enhancers	Fetal Heart	heart
30	chr3:101656000-101662400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:101656000-101662400	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr3:101656200-101658600	Enhancers	Muscle Satellite Cultured Cells	--
33	chr3:101656200-101658600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:101656200-101659200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:101656200-101659600	Weak transcription	A549	lung
36	chr3:101656200-101662800	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr3:101656400-101658200	Weak transcription	NHEK	skin
38	chr3:101656600-101659200	Enhancers	K562	blood
39	chr3:101656800-101658600	Enhancers	Fetal Lung	lung
40	chr3:101656800-101658600	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr3:101656800-101659200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:101657000-101659200	Enhancers	HMEC	breast
43	chr3:101657000-101661400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:101657200-101659200	Enhancers	NHLF	lung
45	chr3:101657400-101658400	Enhancers	Liver	Liver
46	chr3:101657400-101658600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:101657400-101658600	Enhancers	NH-A	brain
48	chr3:101657400-101659600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:101657400-101661200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:101657600-101658600	Weak transcription	Left Ventricle	heart

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