Variant report

Variant	rs12746325
Chromosome Location	chr1:86252025-86252026
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1010058	1.00[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs10747325	1.00[CHB][hapmap]
rs10873722	0.94[ASN][1000 genomes]
rs10873723	0.97[ASN][1000 genomes]
rs10873725	0.89[ASN][1000 genomes]
rs11161676	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11161677	1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs11161678	0.94[ASN][1000 genomes]
rs11161682	0.92[ASN][1000 genomes]
rs11161684	0.94[ASN][1000 genomes]
rs11161685	0.94[ASN][1000 genomes]
rs11161686	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs11161687	1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs11161689	0.82[JPT][hapmap]
rs11161691	0.81[LWK][hapmap]
rs11579570	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590890	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12077825	0.84[ASN][1000 genomes]
rs12088004	0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs12091504	0.82[JPT][hapmap]
rs12091583	1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs12098168	0.84[ASN][1000 genomes]
rs12119620	0.97[ASN][1000 genomes]
rs12128605	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136958	1.00[CHB][hapmap]
rs12240129	0.82[JPT][hapmap]
rs12723176	0.82[JPT][hapmap]
rs12725350	0.82[JPT][hapmap]
rs12727503	0.82[JPT][hapmap]
rs12727784	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12727916	0.94[ASN][1000 genomes]
rs12732365	0.82[JPT][hapmap]
rs12736249	0.82[JPT][hapmap]
rs12739200	0.82[JPT][hapmap]
rs12740060	0.82[JPT][hapmap]
rs12745489	0.82[JPT][hapmap]
rs12747217	0.82[JPT][hapmap]
rs12753056	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12753255	0.82[JPT][hapmap]
rs12755570	0.82[JPT][hapmap]
rs12759687	0.82[JPT][hapmap]
rs12760458	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1325260	1.00[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1481199	0.84[ASN][1000 genomes]
rs17404261	1.00[CHB][hapmap]
rs1842579	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs2170331	0.82[JPT][hapmap];0.81[LWK][hapmap]
rs2297744	0.81[ASN][1000 genomes]
rs4912437	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs4912446	0.82[ASN][1000 genomes]
rs6576790	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs6576791	0.84[ASN][1000 genomes]
rs6576792	0.94[ASN][1000 genomes]
rs6657706	0.82[JPT][hapmap]
rs6665006	0.82[JPT][hapmap]
rs6677315	0.97[ASN][1000 genomes]
rs6693669	1.00[CHD][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs6697619	0.84[ASN][1000 genomes]
rs6698139	1.00[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs6698633	0.94[ASN][1000 genomes]
rs7520948	0.82[JPT][hapmap]
rs7523196	0.82[JPT][hapmap]
rs7530839	0.82[JPT][hapmap]
rs7539262	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554796	0.82[JPT][hapmap]

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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv546721	chr1:86226352-86392577	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv999743	chr1:86241246-86364846	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12746325	ZNHIT6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86222800-86254400	Weak transcription	Fetal Lung	lung
2	chr1:86239800-86253800	Weak transcription	GM12878-XiMat	blood
3	chr1:86251000-86256400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:86251400-86254200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:86251400-86255200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:86252000-86256600	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links