Variant report

Variant	rs4960108
Chromosome Location	chr6:5589242-5589243
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:5588695..5591469-chr6:5650044..5652153,2	K562	blood:
2	chr6:5589204..5591422-chr6:5608593..5611339,2	K562	blood:
3	chr6:5579091..5581648-chr6:5587396..5590119,2	K562	blood:

Variant related genes	Relation type
ENSG00000218574	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1985346	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2013289	0.83[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2064109	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2142736	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2326648	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2326649	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2326651	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4960102	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]
rs4960106	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs4960107	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5012511	0.83[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6597144	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6597146	0.83[EUR][1000 genomes]
rs6597147	0.91[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6903542	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6941763	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7738509	0.94[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs7739718	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7744153	0.94[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7744367	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7744837	0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7765047	0.94[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7765256	0.89[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9328318	0.94[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9328319	0.94[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9328320	0.94[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9378972	0.83[JPT][hapmap]
rs9392084	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9392698	0.80[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9405276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9405852	0.91[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9405853	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9502320	0.83[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.84[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	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	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
4	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
5	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
6	nsv970722	chr6:5588680-5593976	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5577400-5639800	Weak transcription	Fetal Intestine Small	intestine
2	chr6:5581000-5614200	Weak transcription	Lung	lung
3	chr6:5581000-5640400	Weak transcription	Gastric	stomach
4	chr6:5582200-5595000	Weak transcription	Fetal Stomach	stomach
5	chr6:5584600-5589400	Weak transcription	Fetal Lung	lung
6	chr6:5585000-5590200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:5585400-5593200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:5586800-5591200	Weak transcription	Primary T cells from cord blood	blood
9	chr6:5587000-5595200	Weak transcription	Spleen	Spleen
10	chr6:5587200-5619400	Weak transcription	Primary B cells from cord blood	blood
11	chr6:5589000-5591200	Enhancers	Fetal Heart	heart

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