Variant report

Variant	rs1920383
Chromosome Location	chr3:115764342-115764343
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11918028	0.96[CEU][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12485818	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12495426	0.81[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13065579	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1920382	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920384	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1920385	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1920388	0.87[CEU][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2141626	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2141627	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2141629	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4131452	0.86[JPT][hapmap]
rs4240164	0.93[CHD][hapmap];0.87[TSI][hapmap]
rs4286426	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs4398428	0.84[CEU][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs4399891	0.86[JPT][hapmap]
rs4518124	0.92[CHD][hapmap]
rs4611819	0.93[CHD][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs4831218	0.89[CHD][hapmap]
rs4831219	0.93[CHD][hapmap]
rs6438296	0.88[CEU][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs6776244	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6787687	0.84[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6787872	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6789600	0.80[AMR][1000 genomes]
rs6795318	0.84[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6807809	0.88[CEU][hapmap];0.84[JPT][hapmap]
rs7610371	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7625191	0.87[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7632252	0.90[EUR][1000 genomes]
rs9289034	0.89[CHD][hapmap];0.86[JPT][hapmap]
rs9289039	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9289040	0.81[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9840787	0.89[CHD][hapmap]
rs9845521	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9848298	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9863087	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9869887	0.92[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9878286	0.84[CEU][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]

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	nsv931948	chr3:114884574-115802562	Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2760762	chr3:115476222-115807650	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv829685	chr3:115643521-115812913	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1012260	chr3:115680931-115935968	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv2756413	chr3:115721898-115908480	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1001538	chr3:115746561-115791116	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1920383	C3orf15	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115753200-115765000	Weak transcription	Brain Angular Gyrus	brain
2	chr3:115753800-115767400	Weak transcription	Fetal Lung	lung
3	chr3:115754000-115770400	Weak transcription	Brain Substantia Nigra	brain
4	chr3:115754200-115765400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:115758000-115772800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:115758800-115769800	Weak transcription	NHEK	skin
7	chr3:115759000-115765400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:115759000-115778200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:115762000-115769000	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:115762800-115766000	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr3:115764200-115765800	Enhancers	K562	blood

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