Variant report

Variant	rs12119445
Chromosome Location	chr1:85467130-85467131
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12129308	0.80[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap]
rs12730329	0.83[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs12755226	0.83[CEU][hapmap]
rs3754270	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs3850429	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4123223	0.80[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap]
rs473957	0.82[CEU][hapmap]
rs4907117	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs498429	0.80[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.80[MEX][hapmap]
rs504504	0.80[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.80[MEX][hapmap]
rs507465	0.82[CHB][hapmap]
rs536609	0.80[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.80[MEX][hapmap]
rs541897	0.80[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap]
rs55997821	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs597630	0.80[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap]
rs597704	0.80[CHB][hapmap]
rs600924	0.80[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap]
rs645435	0.81[CHB][hapmap]
rs654666	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs657309	0.80[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.80[MEX][hapmap]
rs6576739	0.83[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6674050	0.83[CEU][hapmap]
rs673998	0.80[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.80[MEX][hapmap]
rs674647	0.80[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.80[MEX][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12119445	MCOLN2	cis	multi-tissue	Pritchard
rs12119445	MCOLN2	cis	Thyroid	GTEx
rs12119445	MCOLN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85466800-85467800	Flanking Active TSS	GM12878-XiMat	blood
2	chr1:85466800-85468200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:85467000-85467200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
4	chr1:85467000-85467400	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr1:85467000-85467400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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