Variant report

Variant	rs8031241
Chromosome Location	chr15:40034412-40034413
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1021410	0.92[CEU][hapmap]
rs1021411	0.88[CEU][hapmap]
rs1166716	1.00[CEU][hapmap]
rs1166718	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1166722	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1166723	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12592687	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1565559	0.89[CEU][hapmap]
rs1565561	0.88[CEU][hapmap]
rs1688087	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1844863	0.87[CEU][hapmap]
rs1906163	1.00[CEU][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs1906164	0.89[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs2029584	0.85[CEU][hapmap]
rs2576929	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2576932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2576933	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2631714	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638009	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34943556	0.81[ASN][1000 genomes]
rs4115216	1.00[CHB][hapmap];0.87[JPT][hapmap];0.96[ASN][1000 genomes]
rs4924385	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4924389	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4924391	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs592172	0.85[ASN][1000 genomes]
rs594863	0.89[CHD][hapmap]
rs606927	0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs6492914	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6492915	0.91[CHB][hapmap];0.87[ASN][1000 genomes]
rs6492919	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs66496275	0.81[ASN][1000 genomes]
rs670748	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7179417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7179742	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs7179838	0.89[CEU][hapmap]
rs7180846	0.92[CEU][hapmap]
rs8033485	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8033957	0.91[CHB][hapmap];0.87[CHD][hapmap];0.89[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	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8031241	C15orf54	cis	cerebellum	SCAN
rs8031241	GJD2	cis	cerebellum	SCAN
rs8031241	RPAP1	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40021800-40038000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:40029000-40037200	Weak transcription	Right Atrium	heart
3	chr15:40029200-40040200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr15:40029600-40038600	Weak transcription	NHDF-Ad	bronchial
5	chr15:40032600-40035400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:40033200-40035200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr15:40033400-40034800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr15:40033400-40035000	Enhancers	Adipose Nuclei	Adipose
9	chr15:40033600-40040200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:40034000-40034600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:40034200-40035200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr15:40034400-40038400	Weak transcription	Osteobl	bone

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