Variant report

Variant	rs10443172
Chromosome Location	chr1:85485768-85485769
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10782537	0.87[GIH][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12024977	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs12028736	0.85[ASN][1000 genomes]
rs12030730	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs12030837	0.92[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs12037219	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs12041012	0.84[ASN][1000 genomes]
rs12042160	0.88[ASN][1000 genomes]
rs1371140	0.90[JPT][hapmap]
rs1371143	0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap]
rs1837329	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2028304	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2083283	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs2304641	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2840050	0.92[CHB][hapmap]
rs61768854	0.82[ASN][1000 genomes]
rs61770879	0.88[ASN][1000 genomes]
rs6665436	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs6672362	0.84[CHB][hapmap]
rs6679539	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs6688354	0.85[ASN][1000 genomes]
rs6690464	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6690583	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6700723	0.84[ASN][1000 genomes]
rs7522239	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs7547224	0.92[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs7547317	0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs893618	0.84[ASN][1000 genomes]
rs898036	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[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	nsv830448	chr1:85294094-85491110	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10443172	MCOLN2	cis	parietal	SCAN
rs10443172	LOC339524	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85481800-85487200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:85482600-85487600	Weak transcription	HMEC	breast
3	chr1:85483600-85494800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:85483800-85488800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:85485000-85486000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:85485000-85486000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:85485000-85486400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:85485000-85486400	Strong transcription	Fetal Intestine Small	intestine
9	chr1:85485200-85486400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:85485200-85486400	Enhancers	NHDF-Ad	bronchial
11	chr1:85485400-85485800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:85485400-85491400	Strong transcription	Fetal Intestine Large	intestine
13	chr1:85485400-85513000	Weak transcription	Pancreas	Pancrea
14	chr1:85485600-85486400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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