Variant report

Variant	rs7180846
Chromosome Location	chr15:40062884-40062885
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1021410	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1021411	0.96[CEU][hapmap];0.88[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1027232	0.80[CHB][hapmap]
rs1166716	0.92[CEU][hapmap]
rs1166718	0.81[EUR][1000 genomes]
rs1166722	0.83[EUR][1000 genomes]
rs1166723	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs11858148	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs12437837	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs12440567	0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs1491624	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1565559	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1565561	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16969789	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs16969802	0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs1844863	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1906163	0.92[CEU][hapmap]
rs1906164	0.81[CEU][hapmap]
rs1906166	0.81[ASN][1000 genomes]
rs2029584	0.80[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2171312	0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs2576932	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2576933	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2631714	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2631717	0.81[ASN][1000 genomes]
rs2638009	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs28450006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28538495	0.85[ASN][1000 genomes]
rs28884199	0.85[ASN][1000 genomes]
rs28896916	0.85[ASN][1000 genomes]
rs34320375	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35652496	0.98[ASN][1000 genomes]
rs4924387	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs4924388	0.85[ASN][1000 genomes]
rs4924389	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs4924390	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924392	0.86[ASN][1000 genomes]
rs55639610	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59434895	0.83[ASN][1000 genomes]
rs60431166	0.83[ASN][1000 genomes]
rs61695850	0.83[ASN][1000 genomes]
rs62004808	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492914	0.92[CEU][hapmap]
rs7179417	0.92[CEU][hapmap]
rs7179742	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7179838	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026892	0.82[ASN][1000 genomes]
rs8031241	0.92[CEU][hapmap]

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	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
2	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
3	nsv832979	chr15:40041928-40218407	Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7180846	RPAP1	cis	parietal	SCAN
rs7180846	C15orf54	cis	cerebellum	SCAN
rs7180846	ACTC1	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40040800-40063400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:40052200-40063600	Weak transcription	Brain Angular Gyrus	brain
3	chr15:40053400-40069400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:40054400-40069400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:40056200-40063000	Weak transcription	Esophagus	oesophagus
6	chr15:40058200-40063000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr15:40058200-40063200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:40059000-40063000	Weak transcription	Right Atrium	heart
9	chr15:40059400-40074400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:40060200-40063000	Weak transcription	Fetal Stomach	stomach
11	chr15:40060400-40063000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:40060400-40063400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:40060600-40063000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr15:40062600-40063400	Enhancers	NHDF-Ad	bronchial
15	chr15:40062600-40063800	Enhancers	NHLF	lung
16	chr15:40062800-40063200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:40062800-40063400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:40062800-40063400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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