Variant report

Variant	rs12405767
Chromosome Location	chr1:85746472-85746473
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85744913..85746846-chr1:85930995..85932650,2	MCF-7	breast:
2	chr1:85745110..85747638-chr1:85749252..85751382,2	K562	blood:
3	chr1:85744748..85747168-chr1:85749238..85751854,3	MCF-7	breast:
4	chr1:85739584..85746681-chr1:86042287..86049012,10	K562	blood:
5	chr1:85739297..85743309-chr1:85744628..85748559,4	MCF-7	breast:
6	chr1:85741114..85742845-chr1:85745052..85746553,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264380	Chromatin interaction
ENSG00000272691	Chromatin interaction
ENSG00000153904	Chromatin interaction
ENSG00000223653	Chromatin interaction
ENSG00000142871	Chromatin interaction
ENSG00000142867	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10747317	0.90[CHB][hapmap]
rs10782542	0.80[CHB][hapmap]
rs10782543	0.90[CHB][hapmap]
rs11161573	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs11161585	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11161586	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11161588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11161592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11576939	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs11580090	0.94[ASN][1000 genomes]
rs11583827	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11587512	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11590047	0.87[ASN][1000 genomes]
rs12061305	0.82[ASN][1000 genomes]
rs12061512	0.93[ASN][1000 genomes]
rs12084253	0.85[ASN][1000 genomes]
rs12093484	1.00[CHB][hapmap]
rs12403960	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12754032	0.87[ASN][1000 genomes]
rs17125445	1.00[CHB][hapmap]
rs34743622	0.87[ASN][1000 genomes]
rs4949927	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs4949928	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs55808228	0.85[ASN][1000 genomes]
rs57483398	0.84[ASN][1000 genomes]
rs60325409	0.91[ASN][1000 genomes]
rs61771982	0.81[ASN][1000 genomes]
rs6668948	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6670921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7554249	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs9432848	0.90[CHB][hapmap]

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:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85742800-85763000	Weak transcription	Ovary	ovary
2	chr1:85743000-85747400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:85743000-85749200	Weak transcription	Fetal Stomach	stomach
4	chr1:85743000-85749200	Weak transcription	Psoas Muscle	Psoas
5	chr1:85743000-85773600	Weak transcription	Right Atrium	heart
6	chr1:85743200-85747800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:85743200-85747800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:85743200-85747800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:85743200-85748000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:85743200-85748200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:85743200-85752000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:85743400-85748000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:85743400-85748000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:85745200-85747000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:85745200-85747200	Enhancers	NHDF-Ad	bronchial
16	chr1:85745200-85747600	Strong transcription	Primary B cells from cord blood	blood
17	chr1:85745200-85753600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr1:85745400-85746600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:85745400-85746800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:85745400-85746800	Weak transcription	NHLF	lung
21	chr1:85745400-85747000	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr1:85745400-85747200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:85745400-85749000	Weak transcription	A549	lung
24	chr1:85745400-85749200	Weak transcription	Colonic Mucosa	Colon
25	chr1:85745400-85749400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:85745600-85748000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr1:85745600-85748000	Weak transcription	HepG2	liver
28	chr1:85745600-85748200	Weak transcription	Esophagus	oesophagus
29	chr1:85745600-85749000	Weak transcription	Stomach Mucosa	stomach
30	chr1:85745600-85749200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:85745600-85749200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:85745600-85749400	Weak transcription	Gastric	stomach
33	chr1:85745600-85749400	Weak transcription	Pancreas	Pancrea
34	chr1:85745800-85746600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:85745800-85746800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:85745800-85749000	Weak transcription	HMEC	breast
37	chr1:85745800-85749200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:85745800-85749400	Weak transcription	Lung	lung
39	chr1:85745800-85749600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:85746000-85748000	Weak transcription	NHEK	skin
41	chr1:85746200-85747400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:85746400-85747000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links