Variant report

Variant	rs10877232
Chromosome Location	chr12:59578868-59578869
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	chr12:59577181..59579768-chr12:59589219..59591001,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10747833	0.89[EUR][1000 genomes]
rs10783945	0.96[EUR][1000 genomes]
rs10877217	0.93[EUR][1000 genomes]
rs10877218	0.95[EUR][1000 genomes]
rs10877219	0.95[EUR][1000 genomes]
rs10877220	0.95[EUR][1000 genomes]
rs10877221	0.95[EUR][1000 genomes]
rs10877229	0.98[EUR][1000 genomes]
rs10877230	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877233	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10877237	0.96[EUR][1000 genomes]
rs10877244	0.96[EUR][1000 genomes]
rs10877245	0.93[EUR][1000 genomes]
rs10877249	0.91[EUR][1000 genomes]
rs10877261	0.89[EUR][1000 genomes]
rs11172923	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172925	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172948	0.96[EUR][1000 genomes]
rs11172949	0.96[EUR][1000 genomes]
rs11172950	0.96[EUR][1000 genomes]
rs11172969	0.94[EUR][1000 genomes]
rs11172970	0.94[EUR][1000 genomes]
rs11172974	0.94[EUR][1000 genomes]
rs11614578	0.88[EUR][1000 genomes]
rs12322225	0.95[EUR][1000 genomes]
rs12371751	0.88[EUR][1000 genomes]
rs12371777	0.88[EUR][1000 genomes]
rs12372677	0.93[EUR][1000 genomes]
rs12424141	1.00[ASN][1000 genomes]
rs12426503	1.00[ASN][1000 genomes]
rs12426529	1.00[ASN][1000 genomes]
rs12426936	1.00[ASN][1000 genomes]
rs12426958	1.00[ASN][1000 genomes]
rs1500035	1.00[ASN][1000 genomes]
rs1850127	1.00[ASN][1000 genomes]
rs2036303	0.96[EUR][1000 genomes]
rs2063846	0.95[EUR][1000 genomes]
rs35087760	1.00[ASN][1000 genomes]
rs3913372	1.00[ASN][1000 genomes]
rs60055169	1.00[ASN][1000 genomes]
rs60819410	1.00[ASN][1000 genomes]
rs66833395	0.96[EUR][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	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
2	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
3	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
4	nsv1054961	chr12:59516659-59764209	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv541506	chr12:59516659-59764209	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv559052	chr12:59532203-59809256	Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1050375	chr12:59550900-59655366	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv832430	chr12:59552811-59658333	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1039996	chr12:59556074-59645306	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv559053	chr12:59563004-59643856	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv899127	chr12:59575430-59683281	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10877232	AVIL	cis	cerebellum	SCAN
rs10877232	OR6C2	cis	parietal	SCAN
rs10877232	STAT6	cis	parietal	SCAN
rs10877232	MESP2	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59578400-59579000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr12:59578400-59579000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:59578600-59580400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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