Variant report

Variant	rs2386956
Chromosome Location	chr20:24516109-24516110
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:24511434..24514163-chr20:24516038..24517958,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs13041310	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1555892	0.89[CEU][hapmap];0.84[GIH][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2386954	0.80[CEU][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap]
rs4283490	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6036832	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6049755	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6049757	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6049758	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6049759	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6049760	1.00[CEU][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6049765	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6049768	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6049771	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6049775	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6076233	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6076235	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6114752	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6114757	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6114760	0.85[GIH][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs6114768	0.89[ASW][hapmap];0.85[CEU][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6132742	0.89[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132743	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138316	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][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	nsv1058146	chr20:24210196-24531087	Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2386956	CST9	cis	parietal	SCAN
rs2386956	CST5	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24504000-24525800	Weak transcription	Aorta	Aorta
2	chr20:24508200-24523800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr20:24510800-24518000	Weak transcription	Gastric	stomach
4	chr20:24510800-24525200	Weak transcription	Left Ventricle	heart
5	chr20:24511400-24516200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr20:24513200-24516600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr20:24514800-24525800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr20:24515000-24516800	Enhancers	Brain Hippocampus Middle	brain
9	chr20:24515000-24517200	Enhancers	Brain Substantia Nigra	brain
10	chr20:24515200-24517200	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr20:24515400-24517400	Enhancers	Brain Angular Gyrus	brain
12	chr20:24515800-24516800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr20:24515800-24524800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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