Variant report

Variant	rs10780645
Chromosome Location	chr9:86661654-86661655
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	chr9:86593417..86595634-chr9:86660719..86663662,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165119	Chromatin interaction
ENSG00000178966	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10746729	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10780643	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10780644	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11140280	1.00[CHB][hapmap]
rs11140288	1.00[CHB][hapmap]
rs11140291	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs11140294	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs11140308	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs11140310	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs11140314	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11140316	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs11140337	1.00[ASN][1000 genomes]
rs11140338	1.00[ASN][1000 genomes]
rs11140343	0.87[ASN][1000 genomes]
rs11140344	0.87[ASN][1000 genomes]
rs11140347	0.87[ASN][1000 genomes]
rs11531847	1.00[ASN][1000 genomes]
rs11533022	1.00[ASN][1000 genomes]
rs11533047	1.00[ASN][1000 genomes]
rs11535577	1.00[ASN][1000 genomes]
rs12235653	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12237297	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs167203	0.86[CEU][hapmap]
rs296886	1.00[ASW][hapmap];0.86[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap]
rs296894	0.93[CEU][hapmap];0.97[GIH][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap]
rs3750407	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs55692426	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55714514	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7853235	1.00[ASW][hapmap];0.92[CEU][hapmap];0.97[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7853377	0.86[CEU][hapmap]
rs930340	0.93[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv893514	chr9:86584160-86678917	Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv614762	chr9:86625243-86700593	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3446160	chr9:86661573-86668797	Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10780645	LOC440173	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
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