Variant report

Variant	rs6945478
Chromosome Location	chr7:150425351-150425352
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11762727	0.83[GIH][hapmap];0.84[JPT][hapmap]
rs11983675	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12703097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13240273	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13240287	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13247782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17173582	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1860871	0.88[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2041574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075078	0.92[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs2109999	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2159842	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286900	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2293172	0.83[GIH][hapmap]
rs2373802	0.84[JPT][hapmap]
rs2373850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34443555	0.80[AMR][1000 genomes]
rs34531981	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35370936	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35662160	0.86[EUR][1000 genomes]
rs3735077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3735078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62490382	0.85[EUR][1000 genomes]
rs62490385	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67727004	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6971135	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6978252	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7798682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9690530	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9691508	0.83[GIH][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	esv2758617	chr7:150251949-150463804	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2759573	chr7:150251949-150463804	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv1030109	chr7:150312916-150701010	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv967475	chr7:150323577-150610034	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv831187	chr7:150325913-150503500	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6945478	TMEM176A	cis	cerebellum	SCAN
rs6945478	CNTNAP2	cis	cerebellum	SCAN
rs6945478	IAN4L1	cis	multi-tissue	Pritchard
rs6945478	GIMAP5	cis	lymphoblastoid	seeQTL
rs6945478	TMEM176B	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150422000-150433600	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr7:150423200-150425400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr7:150423200-150426000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
4	chr7:150423800-150425400	Enhancers	Liver	Liver
5	chr7:150424400-150426400	ZNF genes & repeats	Dnd41	blood
6	chr7:150424600-150425400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
7	chr7:150424800-150425600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
8	chr7:150425000-150425400	Enhancers	Fetal Intestine Large	intestine
9	chr7:150425000-150432600	Weak transcription	Thymus	Thymus

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