Variant report

Variant	rs9292665
Chromosome Location	chr5:37649642-37649643
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10461983	0.88[ASN][1000 genomes]
rs10461984	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs10805626	0.81[CHB][hapmap]
rs1084336	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10941361	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.91[ASN][1000 genomes]
rs11749343	0.83[ASN][1000 genomes]
rs11749345	0.86[ASN][1000 genomes]
rs12513493	0.88[ASN][1000 genomes]
rs12516086	0.81[CHB][hapmap]
rs12517792	0.91[ASN][1000 genomes]
rs12519774	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.88[ASN][1000 genomes]
rs12520294	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12521092	0.88[ASN][1000 genomes]
rs12651803	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12656733	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12657090	0.85[CHB][hapmap]
rs13154033	0.91[ASN][1000 genomes]
rs13159969	0.88[ASN][1000 genomes]
rs13171010	0.91[ASN][1000 genomes]
rs13182520	0.85[ASN][1000 genomes]
rs13182737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13185923	0.83[ASN][1000 genomes]
rs13187416	0.91[ASN][1000 genomes]
rs1363925	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs16903666	0.83[CHB][hapmap]
rs1862577	0.88[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.84[ASN][1000 genomes]
rs1874178	0.83[CHB][hapmap]
rs2973086	0.89[ASW][hapmap]
rs4431371	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4869542	0.88[ASN][1000 genomes]
rs505053	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs515404	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs525463	0.83[CHB][hapmap]
rs581376	0.85[CEU][hapmap];0.83[CHB][hapmap]
rs665327	0.87[ASW][hapmap];0.90[CEU][hapmap];0.83[CHB][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes]
rs677084	0.87[ASW][hapmap];0.90[CEU][hapmap];0.83[CHB][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes]
rs682825	0.83[CHB][hapmap]
rs6897494	0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap]
rs7700431	0.83[CHB][hapmap]
rs781794	0.90[CEU][hapmap];0.83[CHB][hapmap];0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026554	chr5:37112133-37734859	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv537726	chr5:37112133-37734859	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv949716	chr5:37179341-37967352	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv1015983	chr5:37240827-37666601	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	nsv1023871	chr5:37330018-37804744	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv537729	chr5:37330018-37804744	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv432744	chr5:37374124-37743077	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1034094	chr5:37406859-37666704	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv537731	chr5:37406859-37666704	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv597846	chr5:37430215-37813591	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv880890	chr5:37443079-37681646	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1030250	chr5:37478163-37734859	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv881383	chr5:37485316-37773877	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9292665	GDNF	cis	cerebellum	SCAN
rs9292665	C5orf42	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37640400-37650800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr5:37647000-37665400	Weak transcription	Primary B cells from cord blood	blood
3	chr5:37648000-37666000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:37649400-37650800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr5:37649600-37650400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:37649600-37652000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr5:37649600-37654200	Weak transcription	Primary T cells from cord blood	blood

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