Variant report

Variant	rs12087340
Chromosome Location	chr1:85746993-85746994
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85745110..85747638-chr1:85749252..85751382,2	K562	blood:
2	chr1:85742898..85744863-chr1:85746512..85748542,2	MCF-7	breast:
3	chr1:85740526..85742722-chr1:85746661..85748660,2	MCF-7	breast:
4	chr1:85743465..85746291-chr1:85746776..85749038,2	MCF-7	breast:
5	chr1:85744748..85747168-chr1:85749238..85751854,3	MCF-7	breast:
6	chr1:85739297..85743309-chr1:85744628..85748559,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223653	Chromatin interaction
ENSG00000264380	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]
rs1060843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161564	0.93[CHB][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11161581	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs11161583	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11161587	0.87[YRI][hapmap];0.80[ASN][1000 genomes]
rs12065528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066982	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068389	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12084232	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12086970	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12095675	0.82[ASN][1000 genomes]
rs12098111	0.87[YRI][hapmap];0.80[ASN][1000 genomes]
rs12098220	0.87[YRI][hapmap];0.80[ASN][1000 genomes]
rs12562182	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12563515	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs12726649	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs12743302	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12744565	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.93[ASN][1000 genomes]
rs12746169	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17124345	0.93[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs35486093	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35783363	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35798604	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs36116171	0.93[ASN][1000 genomes]
rs4074156	0.93[CHB][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4258258	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6693229	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9887811	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9887812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9887879	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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	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:41 , 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	chr1:85745400-85747000	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr1:85745400-85747200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:85745400-85749000	Weak transcription	A549	lung
21	chr1:85745400-85749200	Weak transcription	Colonic Mucosa	Colon
22	chr1:85745400-85749400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:85745600-85748000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:85745600-85748000	Weak transcription	HepG2	liver
25	chr1:85745600-85748200	Weak transcription	Esophagus	oesophagus
26	chr1:85745600-85749000	Weak transcription	Stomach Mucosa	stomach
27	chr1:85745600-85749200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:85745600-85749200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:85745600-85749400	Weak transcription	Gastric	stomach
30	chr1:85745600-85749400	Weak transcription	Pancreas	Pancrea
31	chr1:85745800-85749000	Weak transcription	HMEC	breast
32	chr1:85745800-85749200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:85745800-85749400	Weak transcription	Lung	lung
34	chr1:85745800-85749600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:85746000-85748000	Weak transcription	NHEK	skin
36	chr1:85746200-85747400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:85746400-85747000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:85746800-85747000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:85746800-85747000	Enhancers	NHLF	lung
40	chr1:85746800-85749000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:85746800-85753600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links