Variant report

Variant	rs6911502
Chromosome Location	chr6:56297568-56297569
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	chr6:56297549-56297673	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000266793	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs11751569	0.90[YRI][hapmap]
rs11753813	0.89[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs11756977	0.83[MEX][hapmap]
rs11757910	0.89[YRI][hapmap]
rs11757941	0.90[YRI][hapmap]
rs11758339	1.00[ASW][hapmap];0.81[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11759493	1.00[ASW][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.80[TSI][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes]
rs12174955	0.80[CEU][hapmap];0.88[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13204556	0.87[AMR][1000 genomes]
rs13218268	0.90[YRI][hapmap]
rs1359068	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1359070	0.82[AMR][1000 genomes]
rs1535612	0.82[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs1547625	0.89[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs1570492	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17825773	0.89[CHB][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.84[ASN][1000 genomes]
rs2273972	0.95[GIH][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2273973	0.82[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs2273974	0.82[CHB][hapmap];0.82[AMR][1000 genomes]
rs2294697	0.90[YRI][hapmap]
rs2397221	1.00[ASW][hapmap];0.90[YRI][hapmap]
rs2397226	0.82[CHB][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes]
rs2894837	0.82[CHB][hapmap];0.94[MEX][hapmap]
rs34954984	0.87[AMR][1000 genomes]
rs35926142	0.82[AMR][1000 genomes]
rs4130060	0.83[YRI][hapmap]
rs4143828	0.91[YRI][hapmap]
rs4236139	0.89[GIH][hapmap];0.88[MEX][hapmap]
rs4236140	0.93[GIH][hapmap];0.94[MEX][hapmap]
rs4236145	0.86[GIH][hapmap];0.83[MEX][hapmap]
rs4283892	0.82[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes]
rs4331988	0.82[AMR][1000 genomes]
rs4454141	0.86[GIH][hapmap];0.94[MEX][hapmap]
rs4499917	0.93[GIH][hapmap];0.83[MEX][hapmap]
rs45486696	0.82[AMR][1000 genomes]
rs4712132	0.86[GIH][hapmap];0.83[MEX][hapmap]
rs4712133	0.82[GIH][hapmap];0.83[MEX][hapmap]
rs4715625	0.82[CHB][hapmap]
rs4715626	0.89[GIH][hapmap];0.94[MEX][hapmap]
rs4715627	0.89[GIH][hapmap];0.88[MEX][hapmap]
rs4715629	0.82[GIH][hapmap];0.83[MEX][hapmap]
rs4715630	1.00[ASW][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.91[YRI][hapmap]
rs4715631	0.82[GIH][hapmap];0.83[MEX][hapmap]
rs58705220	0.84[ASN][1000 genomes]
rs594008	0.81[GIH][hapmap]
rs594435	0.85[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs595238	1.00[YRI][hapmap]
rs606894	0.94[ASN][1000 genomes]
rs607271	0.94[ASN][1000 genomes]
rs636389	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6459161	0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs6459163	0.84[AFR][1000 genomes]
rs656550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs656988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs657057	0.89[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs6904202	0.89[GIH][hapmap];0.81[TSI][hapmap]
rs6911307	0.89[ASN][1000 genomes]
rs6913572	0.82[AMR][1000 genomes]
rs6914325	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6915564	0.81[YRI][hapmap]
rs6916287	0.95[ASN][1000 genomes]
rs6919608	0.89[GIH][hapmap]
rs6927258	0.88[CHB][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72877350	0.87[AMR][1000 genomes]
rs7741295	1.00[ASW][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.91[YRI][hapmap]
rs7746753	0.82[AMR][1000 genomes]
rs7755220	0.94[EUR][1000 genomes]
rs7761281	0.86[GIH][hapmap];0.83[MEX][hapmap]
rs7762629	0.91[YRI][hapmap]
rs7775847	0.90[YRI][hapmap]
rs9296848	0.87[ASW][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes]
rs9349822	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9349823	0.88[CHB][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9349825	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9357918	0.87[ASN][1000 genomes]
rs9370531	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9370533	0.88[CHB][hapmap]
rs9370534	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9370535	0.83[YRI][hapmap];0.87[AMR][1000 genomes]
rs9382631	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9396210	0.95[ASN][1000 genomes]
rs9396211	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9396213	0.88[CHB][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs9396214	0.82[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs9396215	0.85[AMR][1000 genomes]
rs9464388	0.83[ASN][1000 genomes]
rs9475713	0.89[GIH][hapmap];0.83[MEX][hapmap]
rs9475714	0.89[GIH][hapmap];0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv965727	chr6:56294729-56298343	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6911502	TRAM2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56296800-56297600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:56297000-56297800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:56297400-56297800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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