Variant report

Variant	rs2579896
Chromosome Location	chr8:35423547-35423548
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10099855	0.80[ASN][1000 genomes]
rs12541423	0.86[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12546560	0.82[ASN][1000 genomes]
rs12546786	0.85[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs12550037	0.86[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs13250198	0.82[ASN][1000 genomes]
rs1439151	0.80[EUR][1000 genomes]
rs1439157	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16884109	0.82[ASN][1000 genomes]
rs1821958	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1898829	0.82[EUR][1000 genomes]
rs1992251	0.82[ASN][1000 genomes]
rs1992252	0.82[ASN][1000 genomes]
rs2243786	0.81[EUR][1000 genomes]
rs2579885	0.83[EUR][1000 genomes]
rs2579886	0.84[EUR][1000 genomes]
rs2579889	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2579890	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2579892	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2589333	0.83[EUR][1000 genomes]
rs2589347	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2589348	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2589744	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2589749	0.80[EUR][1000 genomes]
rs2589750	0.82[EUR][1000 genomes]
rs2589760	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589764	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2921109	0.80[AMR][1000 genomes]
rs35827990	0.80[ASN][1000 genomes]
rs41360948	0.81[CHB][hapmap]
rs41409549	0.80[ASN][1000 genomes]
rs4739306	0.82[ASN][1000 genomes]
rs6980691	0.82[ASN][1000 genomes]
rs6988474	0.86[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs6997313	0.82[ASN][1000 genomes]
rs7002810	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7002972	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7818666	0.82[ASN][1000 genomes]
rs7845667	0.82[ASN][1000 genomes]
rs983271	0.82[ASN][1000 genomes]
rs983272	0.82[ASN][1000 genomes]
rs983273	0.82[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2579896	LSM1	cis	parietal	SCAN
rs2579896	C8orf86	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:35414800-35424200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:35415000-35431000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr8:35419000-35430200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr8:35419000-35439400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr8:35419000-35439600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr8:35419200-35427600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr8:35423000-35423800	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr8:35423000-35424000	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr8:35423200-35423600	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr8:35423200-35424200	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr8:35423400-35423800	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr8:35423400-35423800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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