Variant report

Variant	rs6049401
Chromosome Location	chr20:24085959-24085960
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	chr20:24084790..24086401-chr20:24090603..24093438,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs55771985	0.87[EUR][1000 genomes]
rs58712671	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs60160675	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6036649	0.94[ASN][1000 genomes]
rs6036659	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6036660	0.91[ASN][1000 genomes]
rs6049396	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049398	0.94[ASN][1000 genomes]
rs6049402	0.94[ASN][1000 genomes]
rs6049404	0.94[ASN][1000 genomes]
rs6049405	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6049406	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6049407	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6049408	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6049409	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6049410	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6049411	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6049420	0.91[ASN][1000 genomes]
rs6049421	0.91[ASN][1000 genomes]
rs6076185	0.93[EUR][1000 genomes]
rs6076187	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6076190	0.87[EUR][1000 genomes]
rs6076194	0.87[EUR][1000 genomes]
rs6083374	0.93[EUR][1000 genomes]
rs6083375	0.93[EUR][1000 genomes]
rs6083376	0.93[EUR][1000 genomes]
rs6083378	0.93[EUR][1000 genomes]
rs6083379	0.93[EUR][1000 genomes]
rs6083382	0.93[EUR][1000 genomes]
rs6083383	0.93[EUR][1000 genomes]
rs6083384	0.93[EUR][1000 genomes]
rs6083386	0.93[EUR][1000 genomes]
rs6083388	0.87[EUR][1000 genomes]
rs6083390	0.87[EUR][1000 genomes]
rs6083391	0.87[EUR][1000 genomes]
rs6083398	0.87[EUR][1000 genomes]
rs6083400	0.87[EUR][1000 genomes]
rs6083404	0.84[EUR][1000 genomes]
rs6106785	0.93[ASN][1000 genomes]
rs6114490	0.89[ASN][1000 genomes]
rs8115661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs962527	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1056491	chr20:23955040-24105080	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24082600-24088000	Enhancers	HUVEC	blood vessel
2	chr20:24083400-24096200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr20:24083600-24086200	Weak transcription	HMEC	breast
4	chr20:24084000-24086600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr20:24084400-24086200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr20:24084400-24086200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr20:24085000-24086000	Weak transcription	NH-A	brain
8	chr20:24085000-24086000	Weak transcription	Osteobl	bone
9	chr20:24085200-24087400	Weak transcription	Liver	Liver
10	chr20:24085600-24086000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr20:24085800-24086200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr20:24085800-24087400	Enhancers	NHEK	skin

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