Variant report

Variant	rs11161546
Chromosome Location	chr1:85668676-85668677
allele	C/G
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	chr1:85668187-85668740	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	GATA3	chr1:85667893-85668898	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
3	POLR2A	chr1:85665706-85668876	PANC-1	pancreas:	n/a	n/a
4	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
5	GATA3	chr1:85668158-85668895	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
6	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
7	GATA3	chr1:85668214-85668764	SH-SY5Y	brain:	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
8	SIN3AK20	chr1:85665469-85668719	MCF-7	breast:	n/a	n/a
9	KAP1	chr1:85667531-85668889	HEK293	kidney:	n/a	n/a
10	GATA3	chr1:85668599-85668874	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	chr1:85664620..85668785-chr1:85722586..85726821,6	MCF-7	breast:
2	chr1:85668441..85670596-chr1:85684602..85686321,2	K562	blood:
3	chr1:85663638..85666684-chr1:85666937..85669926,3	MCF-7	breast:
4	chr1:85665631..85669772-chr1:85739485..85744059,5	K562	blood:
5	chr1:85667789..85671155-chr1:85672864..85676253,5	K562	blood:
6	chr1:85667494..85671075-chr1:85689483..85691213,3	K562	blood:
7	chr1:85666785..85669663-chr1:85715100..85717431,2	K562	blood:
8	chr1:85666946..85668694-chr1:85686380..85689036,2	K562	blood:
9	chr1:85667613..85669609-chr1:85711130..85713411,2	MCF-7	breast:

Variant related genes	Relation type
SYDE2	TF binding region
ENSG00000162642	Chromatin interaction
ENSG00000223653	Chromatin interaction
ENSG00000142867	Chromatin interaction
ENSG00000097096	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11161536	1.00[AMR][1000 genomes]
rs11161537	1.00[AMR][1000 genomes]
rs11161544	1.00[AMR][1000 genomes]
rs12073567	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12075407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12083953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12087427	1.00[AMR][1000 genomes]
rs58859506	1.00[AMR][1000 genomes]
rs72950882	1.00[AMR][1000 genomes]
rs72950887	1.00[AMR][1000 genomes]
rs72950898	1.00[AMR][1000 genomes]
rs72952616	1.00[AMR][1000 genomes]
rs72952618	1.00[AMR][1000 genomes]
rs72952624	1.00[AMR][1000 genomes]
rs72952634	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv3325481	chr1:85666189-85668737	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85661000-85669000	Active TSS	Stomach Smooth Muscle	stomach
2	chr1:85667200-85668800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:85668000-85668800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:85668000-85668800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr1:85668000-85668800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:85668000-85668800	Enhancers	Fetal Intestine Small	intestine
7	chr1:85668000-85669000	Weak transcription	Colonic Mucosa	Colon
8	chr1:85668000-85669000	Enhancers	Small Intestine	intestine
9	chr1:85668000-85669800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:85668000-85670400	Weak transcription	Esophagus	oesophagus
11	chr1:85668000-85671000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:85668000-85671000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr1:85668000-85689000	Weak transcription	Gastric	stomach
14	chr1:85668200-85668800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
15	chr1:85668200-85668800	Enhancers	A549	lung
16	chr1:85668200-85669000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:85668200-85669200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr1:85668200-85670600	Enhancers	NHLF	lung
19	chr1:85668200-85670800	Enhancers	Osteobl	bone
20	chr1:85668400-85668800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:85668400-85668800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:85668400-85668800	Enhancers	Liver	Liver
23	chr1:85668400-85668800	Enhancers	Duodenum Mucosa	Duodenum
24	chr1:85668400-85668800	Enhancers	Fetal Intestine Large	intestine
25	chr1:85668400-85669000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:85668400-85669000	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr1:85668400-85669000	Enhancers	Fetal Lung	lung
28	chr1:85668400-85669000	Active TSS	Rectal Smooth Muscle	rectum
29	chr1:85668400-85669200	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr1:85668400-85669200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:85668400-85669200	Enhancers	Placenta	Placenta
32	chr1:85668400-85669600	Weak transcription	NHEK	skin
33	chr1:85668400-85669800	Enhancers	Adipose Nuclei	Adipose
34	chr1:85668400-85669800	Weak transcription	NHDF-Ad	bronchial
35	chr1:85668400-85670400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:85668400-85670400	Weak transcription	HMEC	breast
37	chr1:85668400-85670600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:85668400-85671200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:85668400-85671200	Enhancers	Hela-S3	cervix
40	chr1:85668400-85677800	Weak transcription	Right Atrium	heart
41	chr1:85668600-85668800	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr1:85668600-85668800	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr1:85668600-85668800	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr1:85668600-85668800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
45	chr1:85668600-85668800	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr1:85668600-85668800	Bivalent/Poised TSS	Primary B cells from cord blood	blood
47	chr1:85668600-85668800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
48	chr1:85668600-85668800	Enhancers	Fetal Stomach	stomach
49	chr1:85668600-85669000	Active TSS	Colon Smooth Muscle	Colon
50	chr1:85668600-85669000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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