Variant report

Variant	rs546202
Chromosome Location	chr11:65510024-65510025
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	chr11:65509973-65510077	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:65477043..65480917-chr11:65508672..65511381,3	MCF-7	breast:
2	chr11:65509847..65512521-chr11:65541079..65543934,2	K562	blood:
3	chr11:65508695..65511331-chr11:65535308..65536839,2	MCF-7	breast:
4	chr11:65508777..65511701-chr11:65625140..65626747,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255557	TF binding region
ENSG00000172977	Chromatin interaction
ENSG00000172757	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10896041	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1193496	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12146493	0.86[CHB][hapmap];0.88[CHD][hapmap];0.85[LWK][hapmap];0.85[YRI][hapmap];0.86[ASN][1000 genomes]
rs12293022	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12801731	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2508301	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2508303	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs478304	0.97[EUR][1000 genomes]
rs495961	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs498354	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs502468	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs509206	0.97[EUR][1000 genomes]
rs522800	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs537786	1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs570954	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs574483	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs603326	0.86[CHB][hapmap]
rs603645	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs610037	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs614771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61895666	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61895677	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs669742	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
2	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
3	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
4	nsv897758	chr11:65490756-65564035	Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv983035	chr11:65494712-65529501	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3389596	chr11:65507376-65510174	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs546202	RNASEH2C	cis	parietal	SCAN
rs546202	MAP3K11	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65495400-65511400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr11:65507800-65511600	Weak transcription	Spleen	Spleen
3	chr11:65509000-65511400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:65509400-65511200	Enhancers	Placenta	Placenta
5	chr11:65509800-65510600	Enhancers	Liver	Liver
6	chr11:65510000-65510400	Enhancers	Fetal Lung	lung
7	chr11:65510000-65510600	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links