Variant report

Variant	rs524995
Chromosome Location	chr11:59929786-59929787
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:59927372-59929977	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr11:59928363-59929961	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:59929729..59931318-chr11:59936371..59938548,3	K562	blood:
2	chr11:59899268..59901225-chr11:59929250..59931810,2	K562	blood:

Variant related genes	Relation type
ENSG00000254952	TF binding region

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10750930	0.89[JPT][hapmap]
rs1286182	0.80[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1294440	0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs1303617	0.80[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1303618	0.96[EUR][1000 genomes]
rs1303619	0.96[EUR][1000 genomes]
rs1303620	0.80[CHD][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1303622	0.80[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1315507	0.96[EUR][1000 genomes]
rs1441585	0.80[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs2243987	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2433240	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2847662	0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs474888	0.96[EUR][1000 genomes]
rs475494	0.96[EUR][1000 genomes]
rs475812	0.89[JPT][hapmap];0.96[EUR][1000 genomes]
rs477352	0.96[EUR][1000 genomes]
rs485682	0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs489297	0.80[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs500886	0.96[EUR][1000 genomes]
rs500888	0.96[EUR][1000 genomes]
rs512548	0.80[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs512555	0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs519743	0.80[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs523806	0.96[EUR][1000 genomes]
rs524755	0.96[EUR][1000 genomes]
rs528421	0.96[EUR][1000 genomes]
rs535413	0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs541468	0.96[EUR][1000 genomes]
rs542665	0.96[EUR][1000 genomes]
rs546840	0.96[EUR][1000 genomes]
rs548515	0.96[EUR][1000 genomes]
rs549633	0.96[EUR][1000 genomes]
rs562442	0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs562637	0.96[EUR][1000 genomes]
rs569108	0.80[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs571582	0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs572084	0.96[EUR][1000 genomes]
rs573305	0.96[EUR][1000 genomes]
rs574060	0.96[EUR][1000 genomes]
rs574700	0.80[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs575103	0.96[EUR][1000 genomes]
rs575930	0.96[EUR][1000 genomes]
rs576295	0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs576483	0.80[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs576616	0.96[EUR][1000 genomes]
rs578269	0.82[JPT][hapmap];0.96[EUR][1000 genomes]
rs581818	0.87[ASN][1000 genomes]
rs585540	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs587634	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs588448	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs590351	0.84[ASN][1000 genomes]
rs590532	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs592496	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs596788	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs597982	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598862	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs600194	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs605820	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs620368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624233	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs625025	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs638872	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs641051	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs641829	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs642426	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs646924	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs653285	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs654443	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs661376	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs662674	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs668095	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs668134	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs670925	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs675316	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs680699	0.84[ASN][1000 genomes]
rs682025	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs682739	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs684977	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832173	chr11:59788884-59940560	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv468579	chr11:59814287-59975400	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv555150	chr11:59814287-59975400	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv33843	chr11:59908131-59945334	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv832174	chr11:59909267-60073908	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs524995	MS4A6A	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59924000-59930800	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr11:59924000-59932800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:59924800-59929800	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr11:59926400-59930000	Enhancers	HUVEC	blood vessel

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