Variant report

Variant	rs427497
Chromosome Location	chr9:107982792-107982793
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10120310	0.98[ASN][1000 genomes]
rs10820792	0.90[CHB][hapmap]
rs10820795	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs10991598	0.90[CHB][hapmap]
rs10991600	0.89[CHB][hapmap]
rs10991601	0.90[CHB][hapmap]
rs10991611	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs10991612	0.90[CHB][hapmap]
rs10991617	0.90[CHB][hapmap]
rs10991618	0.90[CHB][hapmap]
rs12335779	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs12343137	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12347364	0.90[CHB][hapmap]
rs12348136	0.90[CHB][hapmap]
rs170582	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs179177	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs182756	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs193007	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs193008	0.81[CHB][hapmap]
rs193009	0.90[CHB][hapmap]
rs2004725	0.90[CHB][hapmap]
rs2100044	0.90[CHB][hapmap]
rs227887	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs227888	0.90[CHB][hapmap]
rs2900397	0.90[CHB][hapmap]
rs327947	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs327948	0.90[CHB][hapmap]
rs327950	0.90[CHB][hapmap]
rs327955	0.90[CHB][hapmap]
rs327956	0.90[CHB][hapmap];0.86[CHD][hapmap]
rs327958	0.90[CHB][hapmap]
rs327959	0.90[CHB][hapmap]
rs327960	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs327967	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs327976	0.90[CHB][hapmap]
rs327982	0.90[CHB][hapmap]
rs327983	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs327984	0.90[CHB][hapmap]
rs327985	0.88[CHB][hapmap]
rs327987	0.90[CHB][hapmap]
rs327990	0.90[CHB][hapmap]
rs327991	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs327992	0.90[CHB][hapmap];0.86[CHD][hapmap]
rs327993	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs327995	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs327997	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs327999	0.90[CHB][hapmap]
rs328006	0.90[CHB][hapmap]
rs328007	0.90[CHB][hapmap]
rs328008	0.90[CHB][hapmap]
rs328010	0.90[CHB][hapmap]
rs328012	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs328013	0.90[CHB][hapmap];0.95[CHD][hapmap]
rs328014	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs328015	0.90[CHB][hapmap]
rs328018	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs328019	0.90[CHB][hapmap]
rs328022	0.90[CHB][hapmap]
rs364564	0.98[ASN][1000 genomes]
rs365629	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs366018	0.98[ASN][1000 genomes]
rs372554	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs372747	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs375034	0.90[CHB][hapmap]
rs375371	0.98[ASN][1000 genomes]
rs376926	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs378467	0.90[CHB][hapmap]
rs378716	0.98[ASN][1000 genomes]
rs380104	0.90[CHB][hapmap]
rs383126	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs383272	0.90[CHB][hapmap]
rs384924	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs384947	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs386565	0.90[CHB][hapmap]
rs390235	0.98[ASN][1000 genomes]
rs399707	0.98[ASN][1000 genomes]
rs401899	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs405704	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs409595	0.98[ASN][1000 genomes]
rs413598	0.98[ASN][1000 genomes]
rs416573	0.98[ASN][1000 genomes]
rs416641	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs420672	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs420717	0.90[CHB][hapmap]
rs421342	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs421495	0.98[ASN][1000 genomes]
rs422084	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs423477	0.98[ASN][1000 genomes]
rs424495	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs435267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs440290	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs442605	0.90[CHB][hapmap]
rs443094	0.90[CHB][hapmap]
rs453041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs453378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6479305	0.90[CHB][hapmap]
rs7020982	0.81[CHB][hapmap];0.91[CHD][hapmap]
rs7021008	0.89[CHB][hapmap]
rs7039398	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046935	chr9:107414720-108028061	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv893684	chr9:107893629-108001107	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv831678	chr9:107923522-108112813	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893685	chr9:107940737-108083485	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1043466	chr9:107950174-108001988	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv893686	chr9:107968330-108083485	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv893687	chr9:107973277-108083485	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS 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	11 gene(s)	inside rSNPs	diseases
9	nsv893688	chr9:107974761-108083485	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv893689	chr9:107978563-108130606	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs427497	ENPP6	trans	brain	seeQTL
rs427497	CLIC6	trans	brain	seeQTL
rs427497	SLC47A1	trans	brain	seeQTL
rs427497	SLPI	trans	brain	seeQTL
rs427497	FGL2	trans	brain	seeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:107979200-107983200	Weak transcription	Fetal Brain Male	brain
2	chr9:107980000-107989400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:107980600-107983000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:107982200-107984200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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