Variant report

Variant	rs12062414
Chromosome Location	chr1:85529097-85529098
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10782534	1.00[CEU][hapmap]
rs10782536	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10873672	1.00[CEU][hapmap]
rs10873679	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs10873682	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10873683	0.95[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161497	1.00[CEU][hapmap]
rs11161498	1.00[CEU][hapmap]
rs11161513	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11161514	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11161518	0.82[CHB][hapmap]
rs11161525	0.85[CHB][hapmap]
rs11161526	0.86[CHB][hapmap]
rs12022421	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12030990	0.86[CHB][hapmap]
rs12063120	0.86[CHB][hapmap]
rs12130357	1.00[CEU][hapmap]
rs12138711	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2486755	1.00[CEU][hapmap]
rs486751	1.00[CEU][hapmap]
rs4907123	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4907125	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs531423	1.00[CEU][hapmap]
rs589653	1.00[CEU][hapmap]
rs600536	1.00[CEU][hapmap]
rs603746	1.00[CEU][hapmap]
rs625045	1.00[CEU][hapmap]
rs632545	1.00[CEU][hapmap]
rs651916	1.00[CEU][hapmap]
rs6576736	1.00[CEU][hapmap]
rs6677091	1.00[CEU][hapmap]
rs668860	1.00[CEU][hapmap]
rs6691970	1.00[CEU][hapmap]
rs6700622	1.00[CEU][hapmap]
rs677476	1.00[CEU][hapmap]
rs7516625	1.00[CEU][hapmap]
rs7522851	1.00[CEU][hapmap]
rs7534574	0.86[CHB][hapmap]
rs7541684	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12062414	MCOLN2	cis	multi-tissue	Pritchard
rs12062414	MCOLN2	cis	Adipose Subcutaneous	GTEx
rs12062414	MCOLN2	cis	Thyroid	GTEx
rs12062414	MCOLN2	cis	Artery Tibial	GTEx
rs12062414	MCOLN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85528400-85529200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:85528400-85529400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:85528600-85529400	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr1:85528600-85529600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:85528800-85529200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:85528800-85530000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:85529000-85529200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:85529000-85529400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell

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