Variant report

Variant	rs2589764
Chromosome Location	chr8:35364242-35364243
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1439151	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1439157	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1821958	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1898829	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2243786	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2579881	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2579885	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2579886	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2579889	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2579890	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2579892	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2579896	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2589333	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2589347	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2589348	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2589744	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2589749	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2589750	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2589760	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2921109	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2921219	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs873893	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[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	nsv1017085	chr8:34742896-35594241	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv539546	chr8:34742896-35594241	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv520421	chr8:35155517-35479468	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1024397	chr8:35296922-35424277	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv533420	chr8:35358115-36227536	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2589764	C8orf86	cis	parietal	SCAN
rs2589764	ADAM3A	cis	parietal	SCAN
rs2589764	LSM1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:35356400-35391200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr8:35359200-35371600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr8:35359800-35397200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr8:35361600-35366000	Weak transcription	Fetal Brain Female	brain
5	chr8:35362400-35368000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr8:35363200-35365600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links