Variant report

Variant	rs17545406
Chromosome Location	chr2:31653405-31653406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:31647816..31650394-chr2:31651121..31653448,2	K562	blood:
2	chr2:31644783..31646814-chr2:31651303..31655171,3	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1033688	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1033689	0.92[ASN][1000 genomes]
rs1033690	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11124260	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11124261	0.91[ASN][1000 genomes]
rs11526116	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11526117	0.89[ASN][1000 genomes]
rs11674100	0.95[ASN][1000 genomes]
rs11679875	0.88[ASN][1000 genomes]
rs12467131	0.84[ASN][1000 genomes]
rs12468955	0.94[ASN][1000 genomes]
rs12469125	0.92[ASN][1000 genomes]
rs12473298	0.93[ASN][1000 genomes]
rs12479415	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1429372	0.81[CHB][hapmap]
rs17545483	0.95[ASN][1000 genomes]
rs17604588	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17604831	0.94[ASN][1000 genomes]
rs1884723	0.91[ASN][1000 genomes]
rs1978638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1978639	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs206806	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs206811	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs206816	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2163058	0.98[ASN][1000 genomes]
rs2365772	0.95[ASN][1000 genomes]
rs2365778	0.86[ASN][1000 genomes]
rs28810790	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28815209	0.94[ASN][1000 genomes]
rs28879135	0.94[ASN][1000 genomes]
rs34096339	0.88[ASN][1000 genomes]
rs4622775	0.92[ASN][1000 genomes]
rs4952215	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4952236	0.98[ASN][1000 genomes]
rs4952251	0.91[ASN][1000 genomes]
rs4952263	0.88[ASN][1000 genomes]
rs55933129	0.95[ASN][1000 genomes]
rs56247470	0.91[ASN][1000 genomes]
rs56271553	0.87[ASN][1000 genomes]
rs58071748	0.97[ASN][1000 genomes]
rs58364223	0.87[ASN][1000 genomes]
rs58967340	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59770035	0.94[ASN][1000 genomes]
rs59964343	0.97[ASN][1000 genomes]
rs60441502	0.90[ASN][1000 genomes]
rs60989770	0.92[ASN][1000 genomes]
rs61316601	0.87[ASN][1000 genomes]
rs61706447	0.97[ASN][1000 genomes]
rs62141223	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66492775	0.97[ASN][1000 genomes]
rs6710918	0.81[ASN][1000 genomes]
rs67603251	0.93[ASN][1000 genomes]
rs67830899	0.96[ASN][1000 genomes]
rs72790682	0.95[ASN][1000 genomes]
rs72794621	0.87[ASN][1000 genomes]
rs7575607	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585845	0.94[ASN][1000 genomes]
rs7595578	0.97[ASN][1000 genomes]
rs7602067	0.90[ASN][1000 genomes]
rs766273	0.94[ASN][1000 genomes]
rs9636426	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949028	chr2:31502801-31665108	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv456030	chr2:31598823-31820256	Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv456041	chr2:31598823-31820256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv581269	chr2:31598823-31820256	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv998853	chr2:31601455-31858961	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1005565	chr2:31603134-31868877	Genic enhancers Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1007179	chr2:31616112-31835410	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1005032	chr2:31616112-31867450	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1013891	chr2:31629179-31854283	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv535612	chr2:31629179-31854283	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31648600-31654200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr2:31650600-31654200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:31650800-31654400	Enhancers	HMEC	breast
4	chr2:31651000-31654200	Enhancers	NHEK	skin
5	chr2:31651200-31654200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:31651800-31653600	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr2:31651800-31654000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:31652200-31654000	Enhancers	Hela-S3	cervix
9	chr2:31652400-31654000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:31652600-31653600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr2:31652600-31654000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
12	chr2:31652600-31654200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr2:31652800-31653600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr2:31652800-31653800	Enhancers	Stomach Mucosa	stomach
15	chr2:31653000-31653600	Enhancers	Primary hematopoietic stem cells	blood
16	chr2:31653000-31654000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:31653000-31654200	Enhancers	Esophagus	oesophagus
18	chr2:31653000-31654400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:31653200-31653800	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr2:31653400-31669600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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