Variant report

Variant	rs13159540
Chromosome Location	chr5:12343985-12343986
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	chr5:12331301..12333621-chr5:12342570..12344287,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10059121	0.84[EUR][1000 genomes]
rs10072442	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10073418	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11133710	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11133711	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11741576	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11743863	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11746644	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11747484	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11954444	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11955624	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11956485	0.83[EUR][1000 genomes]
rs11959917	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12514692	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12515325	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12520542	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13155688	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13181463	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16902166	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16902167	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2191010	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2215205	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2400150	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2400153	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2401064	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34393964	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35023099	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35086429	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35565362	0.89[EUR][1000 genomes]
rs4368730	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4440360	0.80[ASN][1000 genomes]
rs4552595	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4568365	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4580774	0.83[EUR][1000 genomes]
rs58300588	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554700	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67479936	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6879027	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6887689	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6888210	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6888233	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6892402	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6892563	0.81[ASN][1000 genomes]
rs7700684	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7700838	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7701021	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7701058	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7701108	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7701437	0.83[EUR][1000 genomes]
rs7704704	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7705498	0.81[EUR][1000 genomes]
rs7706464	0.84[EUR][1000 genomes]
rs7726993	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7728133	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7728564	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7729412	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7736714	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7736924	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025096	chr5:12049731-12778382	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv537660	chr5:12049731-12778382	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1030580	chr5:12254774-12364629	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1015676	chr5:12276531-12540904	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv427711	chr5:12285375-12747819	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1026529	chr5:12285675-12387812	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1017000	chr5:12285675-12451819	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv537664	chr5:12285675-12451819	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv917255	chr5:12310838-12929427	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv4716	chr5:12334952-12379645	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv915585	chr5:12336874-12849583	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv597156	chr5:12343985-12464763	Enhancers Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:12331400-12344600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links