Variant report

Variant	rs12073567
Chromosome Location	chr1:85668899-85668900
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	GATA3	chr1:85668119-85668997	MCF-7	breast:	n/a	chr1:85668706-85668713 chr1:85668704-85668713 chr1:85668695-85668712 chr1:85668705-85668713 chr1:85668706-85668713 chr1:85668699-85668720 chr1:85668706-85668713 chr1:85668341-85668351 chr1:85668338-85668354 chr1:85668704-85668713 chr1:85668701-85668717 chr1:85668706-85668717 chr1:85668704-85668714 chr1:85668663-85668674
2	POLR2A	chr1:85668731-85669035	ProgFib	skin:	n/a	n/a
3	GATA3	chr1:85668544-85668914	T-47D	breast:	n/a	chr1:85668706-85668713 chr1:85668704-85668713 chr1:85668695-85668712 chr1:85668705-85668713 chr1:85668706-85668713 chr1:85668699-85668720 chr1:85668706-85668713 chr1:85668704-85668713 chr1:85668701-85668717 chr1:85668706-85668717 chr1:85668704-85668714 chr1:85668663-85668674

No.	Distal block	Cell Line	Cell type
1	chr1:85668441..85670596-chr1:85684602..85686321,2	K562	blood:
2	chr1:85663638..85666684-chr1:85666937..85669926,3	MCF-7	breast:
3	chr1:85665631..85669772-chr1:85739485..85744059,5	K562	blood:
4	chr1:85667789..85671155-chr1:85672864..85676253,5	K562	blood:
5	chr1:85667494..85671075-chr1:85689483..85691213,3	K562	blood:
6	chr1:85666785..85669663-chr1:85715100..85717431,2	K562	blood:
7	chr1:85667613..85669609-chr1:85711130..85713411,2	MCF-7	breast:
8	chr1:85577108..85579673-chr1:85668839..85670943,2	MCF-7	breast:
9	chr1:85668766..85670351-chr1:85680923..85682596,2	MCF-7	breast:

Variant related genes	Relation type
SYDE2	TF binding region
ENSG00000223653	Chromatin interaction
ENSG00000142867	Chromatin interaction
ENSG00000097096	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11161536	0.85[AMR][1000 genomes]
rs11161537	0.85[AMR][1000 genomes]
rs11161544	0.85[AMR][1000 genomes]
rs11161546	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12075407	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12083953	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12087427	0.85[AMR][1000 genomes]
rs58859506	0.85[AMR][1000 genomes]
rs72950882	0.85[AMR][1000 genomes]
rs72950887	0.85[AMR][1000 genomes]
rs72950898	0.85[AMR][1000 genomes]
rs72952616	0.85[AMR][1000 genomes]
rs72952618	0.85[AMR][1000 genomes]
rs72952624	0.85[AMR][1000 genomes]
rs72952634	0.85[AMR][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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85661000-85669000	Active TSS	Stomach Smooth Muscle	stomach
2	chr1:85668000-85669000	Weak transcription	Colonic Mucosa	Colon
3	chr1:85668000-85669000	Enhancers	Small Intestine	intestine
4	chr1:85668000-85669800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:85668000-85670400	Weak transcription	Esophagus	oesophagus
6	chr1:85668000-85671000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:85668000-85671000	Enhancers	Muscle Satellite Cultured Cells	--
8	chr1:85668000-85689000	Weak transcription	Gastric	stomach
9	chr1:85668200-85669000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:85668200-85669200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr1:85668200-85670600	Enhancers	NHLF	lung
12	chr1:85668200-85670800	Enhancers	Osteobl	bone
13	chr1:85668400-85669000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:85668400-85669000	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr1:85668400-85669000	Enhancers	Fetal Lung	lung
16	chr1:85668400-85669000	Active TSS	Rectal Smooth Muscle	rectum
17	chr1:85668400-85669200	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr1:85668400-85669200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:85668400-85669200	Enhancers	Placenta	Placenta
20	chr1:85668400-85669600	Weak transcription	NHEK	skin
21	chr1:85668400-85669800	Enhancers	Adipose Nuclei	Adipose
22	chr1:85668400-85669800	Weak transcription	NHDF-Ad	bronchial
23	chr1:85668400-85670400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:85668400-85670400	Weak transcription	HMEC	breast
25	chr1:85668400-85670600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:85668400-85671200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:85668400-85671200	Enhancers	Hela-S3	cervix
28	chr1:85668400-85677800	Weak transcription	Right Atrium	heart
29	chr1:85668600-85669000	Active TSS	Colon Smooth Muscle	Colon
30	chr1:85668600-85669000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:85668600-85669600	Weak transcription	Fetal Heart	heart
32	chr1:85668600-85672000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:85668600-85680800	Weak transcription	K562	blood
34	chr1:85668800-85669000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:85668800-85669000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:85668800-85669000	Enhancers	Lung	lung
37	chr1:85668800-85669000	Enhancers	Pancreas	Pancrea
38	chr1:85668800-85670400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:85668800-85671200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:85668800-85672000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:85668800-85672000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:85668800-85672000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:85668800-85672200	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links