Variant report

Variant	rs7866883
Chromosome Location	chr9:19030823-19030824
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:19029002..19031851-chr9:19047902..19050642,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155876	Chromatin interaction

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];0.84[YRI][hapmap]
rs10120860	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][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]
rs1932450	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]
rs1932455	1.00[CEU][hapmap]
rs2209777	0.82[ASN][1000 genomes]
rs4607710	1.00[CEU][hapmap]
rs56903563	0.87[AMR][1000 genomes];0.95[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	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73431256	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73433251	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73645550	0.92[ASN][1000 genomes]
rs73645556	0.82[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	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7864679	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7869414	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs7875404	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][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
rs7866883	C9orf138	cis	multi-tissue	Pritchard

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19029000-19031000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr9:19030400-19032200	Weak transcription	Fetal Stomach	stomach
3	chr9:19030800-19031000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr9:19030800-19031000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr9:19030800-19031200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:19030800-19031200	Enhancers	GM12878-XiMat	blood
7	chr9:19030800-19031200	Enhancers	Osteobl	bone
8	chr9:19030800-19031400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:19030800-19031400	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links