Variant report

Variant	rs4960102
Chromosome Location	chr6:5568838-5568839
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1985346	1.00[CEU][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs2013289	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs2064109	0.94[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2142736	1.00[CEU][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2326648	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2326649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2326651	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4960106	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs4960107	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4960108	0.83[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5012511	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6597144	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6597147	0.93[CEU][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6903542	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6941763	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7738509	0.88[CEU][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs7739718	0.87[EUR][1000 genomes]
rs7744153	0.88[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs7744367	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7744837	0.88[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7765047	0.88[CEU][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes]
rs7765256	0.83[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs9328318	0.88[CEU][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs9328319	0.88[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs9328320	0.88[CEU][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs9378972	0.83[JPT][hapmap]
rs9392084	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs9392698	1.00[ASW][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9405276	0.87[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9405852	0.94[CEU][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs9405853	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9502320	1.00[CEU][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer 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	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1034607	chr6:5311590-5573514	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv538120	chr6:5311590-5573514	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv883420	chr6:5524393-5584422	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv5181	chr6:5536921-5581595	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv600887	chr6:5545046-5694713	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1016905	chr6:5566364-5639167	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4960102	KRTAP24-1	trans	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5538000-5573600	Weak transcription	Left Ventricle	heart
2	chr6:5551600-5575200	Weak transcription	Primary B cells from cord blood	blood
3	chr6:5562800-5569800	Weak transcription	Psoas Muscle	Psoas
4	chr6:5565200-5576600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:5565200-5583200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:5567000-5575200	Weak transcription	Primary T cells from cord blood	blood
7	chr6:5567200-5569000	Flanking Active TSS	GM12878-XiMat	blood
8	chr6:5567400-5572800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr6:5568600-5569800	Weak transcription	HepG2	liver
10	chr6:5568800-5570200	Enhancers	Right Atrium	heart

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