Variant report

Variant	rs2501920
Chromosome Location	chr9:79020386-79020387
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10114106	0.84[YRI][hapmap]
rs10114264	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10121699	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10124695	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10735646	0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs10869767	0.84[ASN][1000 genomes]
rs10869773	0.82[ASN][1000 genomes]
rs10869780	0.85[EUR][1000 genomes]
rs11144864	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs11144865	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs11144871	0.82[ASN][1000 genomes]
rs11144880	0.83[ASN][1000 genomes]
rs11788095	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12057052	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13288968	0.88[ASN][1000 genomes]
rs13295433	0.82[ASN][1000 genomes]
rs1535845	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1961995	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2002423	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2251604	0.82[ASN][1000 genomes]
rs2377639	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2490572	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2490574	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2490576	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2490579	0.82[ASN][1000 genomes]
rs2490583	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2490584	0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2490586	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501922	0.81[ASN][1000 genomes]
rs2501923	0.82[ASN][1000 genomes]
rs2501925	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2501927	0.82[ASN][1000 genomes]
rs2501928	0.80[ASN][1000 genomes]
rs2501930	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2501932	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2501937	0.87[ASN][1000 genomes]
rs2501938	0.87[ASN][1000 genomes]
rs2501939	0.87[ASN][1000 genomes]
rs2501940	0.84[EUR][1000 genomes]
rs2501942	0.85[EUR][1000 genomes]
rs3739729	0.82[ASN][1000 genomes]
rs4372070	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs4745541	0.81[ASN][1000 genomes]
rs4745544	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4745545	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4745546	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6560517	0.82[ASN][1000 genomes]
rs6560519	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6560522	0.95[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap]
rs7847608	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7849239	0.82[ASN][1000 genomes]
rs7861089	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893478	chr9:78933874-79101006	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2501920	C9orf40	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79016000-79023000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:79019000-79020400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:79019000-79027600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr9:79019600-79023000	Weak transcription	GM12878-XiMat	blood
5	chr9:79020000-79023000	Weak transcription	Fetal Intestine Small	intestine
6	chr9:79020200-79021000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr9:79020200-79021000	Enhancers	Brain Anterior Caudate	brain

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