Variant report

Variant	rs10880569
Chromosome Location	chr12:44201636-44201637
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:44199055-44202532	GM12891	blood:	n/a	n/a
2	POLR2A	chr12:44199183-44201705	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:44199256-44202422	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:43904994..43906752-chr12:44200364..44202300,2	K562	blood:
2	chr12:44151259..44154357-chr12:44196994..44203443,7	K562	blood:
3	chr12:44201218..44202838-chr6:30582525..30585235,2	MCF-7	breast:
4	chr12:44189560..44194683-chr12:44198050..44201661,11	MCF-7	breast:
5	chr12:44198221..44201924-chr12:44226822..44231143,11	MCF-7	breast:
6	chr12:44151164..44154828-chr12:44196994..44201951,5	K562	blood:
7	chr12:44197117..44201952-chr12:44227919..44231382,13	MCF-7	breast:

No data

Variant related genes	Relation type
TWF1	TF binding region
ENSG00000198001	Chromatin interaction
ENSG00000151239	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000139173	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000129317	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10506231	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10880570	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880571	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11182268	0.89[ASN][1000 genomes]
rs11182269	0.89[ASN][1000 genomes]
rs11182270	0.89[ASN][1000 genomes]
rs11182273	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11182275	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11182279	0.89[ASN][1000 genomes]
rs11182280	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11182281	0.95[ASN][1000 genomes]
rs11182282	0.90[ASN][1000 genomes]
rs11182284	0.90[ASN][1000 genomes]
rs11182286	0.82[ASN][1000 genomes]
rs11182287	0.84[ASN][1000 genomes]
rs11182288	0.90[ASN][1000 genomes]
rs11182289	0.84[ASN][1000 genomes]
rs11182290	0.83[AFR][1000 genomes]
rs11556066	0.89[ASN][1000 genomes]
rs11608602	0.90[ASN][1000 genomes]
rs12226960	0.95[ASN][1000 genomes]
rs12228995	0.81[ASN][1000 genomes]
rs12230695	0.90[ASN][1000 genomes]
rs12231553	0.89[ASN][1000 genomes]
rs12829856	0.89[ASN][1000 genomes]
rs1816854	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28437935	0.85[ASN][1000 genomes]
rs35980560	0.89[ASN][1000 genomes]
rs3764004	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4251562	0.84[ASN][1000 genomes]
rs73093785	0.89[ASN][1000 genomes]
rs7966902	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933142	chr12:44130156-44278300	Active TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44200600-44202000	Weak transcription	Esophagus	oesophagus
2	chr12:44200800-44202000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr12:44201000-44202200	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr12:44201000-44202200	Enhancers	Placenta Amnion	Placenta Amnion
5	chr12:44201000-44205800	Weak transcription	HMEC	breast
6	chr12:44201000-44207400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:44201200-44201800	Enhancers	NHEK	skin
8	chr12:44201200-44202000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:44201200-44206200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:44201400-44201800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:44201400-44202200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:44201400-44204000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr12:44201400-44209400	Weak transcription	Fetal Intestine Small	intestine
14	chr12:44201600-44202000	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr12:44201600-44202000	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr12:44201600-44203800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:44201600-44204400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr12:44201600-44204800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr12:44201600-44205200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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