Variant report

Variant	rs4745012
Chromosome Location	chr9:73080658-73080659
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11142345	0.86[AFR][1000 genomes]
rs11142431	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11142434	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11142435	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11142441	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11142443	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11142451	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11142452	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11142453	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11142454	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11142462	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11142464	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11142465	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11142467	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12238429	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13298975	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1556739	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744598	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4745011	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9644995	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[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	nsv1047862	chr9:72746875-73138287	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription 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 miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv428219	chr9:73006269-73192535	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	nsv831616	chr9:73077855-73220928	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4745012	C9orf85	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:73071400-73081800	Weak transcription	Lung	lung
2	chr9:73071600-73082200	Weak transcription	Pancreas	Pancrea
3	chr9:73072400-73084800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:73077600-73087800	Weak transcription	Gastric	stomach
5	chr9:73078200-73082200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:73079000-73081400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr9:73079200-73081200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr9:73079400-73081000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:73080000-73081000	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr9:73080400-73081000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:73080400-73081200	Enhancers	Adipose Nuclei	Adipose
12	chr9:73080400-73081400	Enhancers	Psoas Muscle	Psoas
13	chr9:73080400-73081400	Enhancers	Right Atrium	heart
14	chr9:73080400-73081400	Enhancers	Right Ventricle	heart
15	chr9:73080400-73082400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:73080400-73082600	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr9:73080400-73083000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:73080400-73083600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:73080400-73086200	Enhancers	Left Ventricle	heart
20	chr9:73080400-73086400	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr9:73080600-73080800	Enhancers	Brain Angular Gyrus	brain
22	chr9:73080600-73080800	Enhancers	Colon Smooth Muscle	Colon
23	chr9:73080600-73081800	Weak transcription	Esophagus	oesophagus
24	chr9:73080600-73084200	Weak transcription	Spleen	Spleen
25	chr9:73080600-73085600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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