Variant report

Variant	rs1948954
Chromosome Location	chr6:54562935-54562936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:54561752..54563922-chr6:54714449..54716896,3	MCF-7	breast:
2	chr6:54558970..54566519-chr6:54708534..54713743,16	MCF-7	breast:
3	chr6:54551257..54553977-chr6:54562035..54564580,2	MCF-7	breast:
4	chr6:54562484..54564963-chr6:54735331..54738094,2	MCF-7	breast:
5	chr6:54559522..54567174-chr6:54707552..54714330,37	MCF-7	breast:
6	chr6:54485033..54487186-chr6:54562620..54564688,2	MCF-7	breast:
7	chr6:54561977..54564257-chr6:54570191..54572297,2	MCF-7	breast:
8	chr6:54562310..54563986-chr6:54587468..54589771,2	MCF-7	breast:
9	chr6:54560989..54563870-chr6:54779771..54781666,2	MCF-7	breast:
10	chr6:54562300..54564099-chr6:54779694..54781853,2	MCF-7	breast:
11	chr6:54561293..54570100-chr6:54582505..54590247,14	MCF-7	breast:
12	chr6:54562847..54563534-chr6:54712448..54713092,2	MCF-7	breast:
13	chr6:54562066..54563606-chr6:54702788..54705608,2	MCF-7	breast:
14	chr6:54559803..54567776-chr6:54579525..54585377,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10948839	0.94[EUR][1000 genomes]
rs10948840	0.84[ASN][1000 genomes]
rs11966577	0.95[EUR][1000 genomes]
rs11967781	1.00[CHB][hapmap]
rs12208090	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap]
rs12525001	0.82[CHB][hapmap]
rs12527080	0.83[CHB][hapmap]
rs12527124	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs12527767	0.86[EUR][1000 genomes]
rs12528270	0.80[ASN][1000 genomes]
rs12528881	0.81[ASN][1000 genomes]
rs12662465	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs1395627	0.93[EUR][1000 genomes]
rs16869519	0.83[CHB][hapmap];0.80[CHD][hapmap];0.84[MEX][hapmap]
rs16885654	0.91[EUR][1000 genomes]
rs16885760	0.93[EUR][1000 genomes]
rs16885866	0.83[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs16885911	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1983140	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2048112	0.81[ASN][1000 genomes]
rs2048113	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34659714	0.95[EUR][1000 genomes]
rs34752465	0.84[ASN][1000 genomes]
rs4712065	0.91[EUR][1000 genomes]
rs4712066	0.92[EUR][1000 genomes]
rs4712068	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs4715466	0.95[EUR][1000 genomes]
rs4715469	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs541689	0.88[EUR][1000 genomes]
rs60501416	0.82[ASN][1000 genomes]
rs61375854	0.93[EUR][1000 genomes]
rs6906715	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs73440097	0.93[EUR][1000 genomes]
rs73442093	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73444113	0.81[ASN][1000 genomes]
rs73444125	0.81[ASN][1000 genomes]
rs7450207	0.95[EUR][1000 genomes]
rs7740110	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs7746312	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7751908	0.81[JPT][hapmap]
rs7753964	0.91[EUR][1000 genomes]
rs7766941	0.88[EUR][1000 genomes]
rs950077	0.95[EUR][1000 genomes]
rs953896	0.95[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54562400-54564200	Enhancers	NHEK	skin
2	chr6:54562400-54565400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr6:54562600-54563200	Enhancers	Placenta Amnion	Placenta Amnion
4	chr6:54562600-54565400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:54562800-54563400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:54562800-54564000	Enhancers	HMEC	breast

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