Variant report

Variant	rs7416239
Chromosome Location	chr1:246885581-246885582
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:246884666..246886259-chr1:246889523..246891914,2	MCF-7	breast:
2	chr1:246876041..246879012-chr1:246883927..246886816,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10127783	1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10159002	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10754532	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10754533	0.86[CHB][hapmap]
rs10802442	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10924820	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10924823	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10924824	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12027222	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12085330	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12090470	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12122102	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs12132038	1.00[ASW][hapmap];1.00[CHB][hapmap]
rs12142760	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12144408	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3007316	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3007317	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3007318	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3007319	1.00[YRI][hapmap]
rs3007322	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3007323	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3007324	1.00[ASW][hapmap];0.88[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3007411	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34649985	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34989088	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3795463	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3795464	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4130316	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4130317	0.87[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4244627	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4244630	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4926454	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4926455	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4926457	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4926459	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs6426323	0.87[CHB][hapmap];0.87[ASN][1000 genomes]
rs6426326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664883	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6685364	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72764626	1.00[ASN][1000 genomes]
rs7364715	0.95[ASN][1000 genomes]
rs7365076	0.85[ASN][1000 genomes]
rs7366377	0.86[ASN][1000 genomes]
rs7417077	0.80[ASN][1000 genomes]
rs7526537	0.83[ASN][1000 genomes]
rs7532928	0.87[CHB][hapmap];0.85[CHD][hapmap]
rs7532929	0.86[ASN][1000 genomes]
rs9426218	0.88[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9426267	0.85[EUR][1000 genomes]
rs9426269	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9426271	0.86[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002805	chr1:246608164-246890518	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv535413	chr1:246608164-246890518	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv870294	chr1:246877043-246927940	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246882200-246886800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links