Variant report

Variant	rs11172758
Chromosome Location	chr12:59238386-59238387
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:59237601..59239530-chr12:59433065..59435700,2	MCF-7	breast:
2	chr12:59237534..59239932-chr12:59242148..59244207,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10877172	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10877174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877176	0.81[CHB][hapmap]
rs10877180	0.81[CHB][hapmap]
rs11172757	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172764	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172766	0.95[AFR][1000 genomes]
rs11172767	0.90[AFR][1000 genomes]
rs11172768	0.93[AFR][1000 genomes]
rs11172769	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11172770	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11172772	0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11514218	0.85[ASN][1000 genomes]
rs11534928	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12227556	0.95[AFR][1000 genomes]
rs12229019	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12367032	0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1846006	0.95[AFR][1000 genomes]
rs1846007	0.95[AFR][1000 genomes]
rs56323549	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59324351	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581221	0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7295313	0.92[AFR][1000 genomes]
rs7305422	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758311	chr12:59022729-59323045	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2759902	chr12:59022729-59323045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv899126	chr12:59199972-59255857	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1052044	chr12:59221968-59238386	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1038273	chr12:59232371-59259628	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11172758	SLC47A2	trans	brain	seeQTL
rs11172758	CAPS	trans	brain	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59235600-59240400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:59235600-59252400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:59236200-59240200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:59237800-59238400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:59237800-59238400	Enhancers	NHEK	skin
6	chr12:59238000-59238400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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