Variant report

Variant	rs2594159
Chromosome Location	chr3:60791815-60791816
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs2064012	0.92[CEU][hapmap]
rs2142296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2205348	0.84[AMR][1000 genomes]
rs2205352	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2205353	0.93[CEU][hapmap];0.84[JPT][hapmap]
rs2251704	0.84[AMR][1000 genomes]
rs2251707	0.84[ASN][1000 genomes]
rs2594160	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2594162	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2594163	0.87[ASN][1000 genomes]
rs2594164	0.84[AMR][1000 genomes]
rs2594165	0.84[AMR][1000 genomes]
rs2594167	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2594168	0.87[ASN][1000 genomes]
rs2594169	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2594170	0.86[AMR][1000 genomes]
rs2594171	0.86[AMR][1000 genomes]
rs2736731	0.86[AMR][1000 genomes]
rs2736734	0.83[ASN][1000 genomes]
rs2736736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2736737	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs4974230	0.85[CEU][hapmap];0.84[CHB][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4974240	0.81[EUR][1000 genomes]
rs6762120	0.85[AMR][1000 genomes]
rs6762122	0.85[AMR][1000 genomes]
rs6764320	0.82[AMR][1000 genomes]
rs9754707	0.86[AMR][1000 genomes]
rs9823013	0.96[CEU][hapmap];0.83[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9878766	0.96[CEU][hapmap];0.84[CHB][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529602	chr3:60088353-60830769	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv998815	chr3:60495872-60830769	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv534038	chr3:60781917-60993082	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv2757872	chr3:60781943-61019003	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2759152	chr3:60781943-61220809	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60790200-60792400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:60790800-60792400	Weak transcription	Brain Germinal Matrix	brain
3	chr3:60790800-60794400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:60790800-60795400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links