Variant report

Variant	rs2596140
Chromosome Location	chr12:122292962-122292963
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10840623	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11043214	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11613865	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1449562	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2596143	1.00[YRI][hapmap]
rs2620334	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2620339	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2707070	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2707072	1.00[YRI][hapmap]
rs2707075	0.93[EUR][1000 genomes]
rs2928283	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34943778	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35384269	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4760102	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4760103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2596140	OASL	cis	parietal	SCAN
rs2596140	RP11-7M8.2	cis	Muscle Skeletal	GTEx
rs2596140	HPD	cis	Muscle Skeletal	GTEx
rs2596140	SUDS3	cis	cerebellum	SCAN
rs2596140	SPPL3	cis	cerebellum	SCAN
rs2596140	CCDC60	cis	parietal	SCAN
rs2596140	HPD	cis	Heart Left Ventricle	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122278200-122294000	Weak transcription	Spleen	Spleen
2	chr12:122278200-122296400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:122278400-122293000	Weak transcription	GM12878-XiMat	blood
4	chr12:122278400-122295400	Weak transcription	Fetal Intestine Small	intestine
5	chr12:122291200-122295400	Weak transcription	Pancreas	Pancrea
6	chr12:122292000-122296400	Weak transcription	Right Atrium	heart
7	chr12:122292200-122294000	Genic enhancers	Liver	Liver
8	chr12:122292200-122296400	Weak transcription	Colonic Mucosa	Colon
9	chr12:122292600-122293400	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr12:122292600-122296000	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr12:122292600-122296000	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr12:122292800-122294400	Weak transcription	HepG2	liver
13	chr12:122292800-122295400	Enhancers	Primary B cells from peripheral blood	blood
14	chr12:122292800-122296400	Weak transcription	Right Ventricle	heart
15	chr12:122292800-122296800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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