Variant report

Variant	rs1932450
Chromosome Location	chr9:19032294-19032295
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10117076	1.00[JPT][hapmap]
rs10120860	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10511664	0.91[ASN][1000 genomes]
rs10511665	1.00[CEU][hapmap]
rs10511666	1.00[CEU][hapmap]
rs10511669	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1932455	1.00[CEU][hapmap]
rs2209777	0.82[ASN][1000 genomes]
rs4607710	1.00[CEU][hapmap]
rs56903563	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56992415	0.82[ASN][1000 genomes]
rs60784683	0.82[ASN][1000 genomes]
rs6475278	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6475284	1.00[CEU][hapmap]
rs6475289	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7019174	1.00[CEU][hapmap]
rs7024953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7025019	1.00[CEU][hapmap]
rs7025316	1.00[CEU][hapmap]
rs7025416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7033648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7038785	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7041472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7043607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs73431244	0.92[ASN][1000 genomes]
rs73431256	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73433251	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73645550	0.92[ASN][1000 genomes]
rs73645556	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73648805	0.82[ASN][1000 genomes]
rs73648807	0.91[ASN][1000 genomes]
rs73648809	0.91[ASN][1000 genomes]
rs73648810	0.91[ASN][1000 genomes]
rs73648811	0.91[ASN][1000 genomes]
rs73648812	0.91[ASN][1000 genomes]
rs73648814	0.91[ASN][1000 genomes]
rs73648815	0.91[ASN][1000 genomes]
rs73648816	0.91[ASN][1000 genomes]
rs7847488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7851358	0.82[ASN][1000 genomes]
rs7860085	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs7862966	0.92[ASN][1000 genomes]
rs7863544	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7864679	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7866883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7869414	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7875404	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892692	chr9:18519699-19045502	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
4	nsv892700	chr9:18979441-19156784	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv892701	chr9:18999837-19032907	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv519909	chr9:19027880-19033376	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1932450	C9orf138	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19031200-19032600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr9:19031400-19032600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr9:19032200-19032600	Enhancers	Fetal Stomach	stomach
4	chr9:19032200-19032800	Bivalent Enhancer	Fetal Intestine Large	intestine

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