Variant report

Variant	rs12063120
Chromosome Location	chr1:85540358-85540359
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85535090..85537602-chr1:85538932..85540814,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1030934	0.84[AMR][1000 genomes]
rs1037742	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10493759	0.86[AMR][1000 genomes]
rs10782534	0.82[CHD][hapmap]
rs10782536	0.81[CHB][hapmap]
rs10782539	0.87[GIH][hapmap];0.84[AMR][1000 genomes]
rs10873679	0.81[CHB][hapmap]
rs10873682	0.81[CHB][hapmap]
rs10873683	0.81[CHB][hapmap]
rs11161514	0.81[CHB][hapmap]
rs11161518	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161519	0.84[ASW][hapmap];0.85[CEU][hapmap];0.89[GIH][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11161520	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11161522	0.84[AMR][1000 genomes]
rs11161525	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11161526	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12022421	0.81[CHB][hapmap]
rs12030990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12062414	0.86[CHB][hapmap]
rs12092036	0.84[AMR][1000 genomes]
rs1417351	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1674173	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1770691	0.89[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs668860	0.82[CHD][hapmap]
rs7517848	0.85[CEU][hapmap]
rs7522343	0.82[AMR][1000 genomes]
rs7523865	0.84[AMR][1000 genomes]
rs7526413	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7528575	0.84[AMR][1000 genomes]
rs7534574	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7536296	0.87[GIH][hapmap];0.84[AMR][1000 genomes]
rs7542253	0.84[AMR][1000 genomes]
rs7547345	0.84[AMR][1000 genomes]
rs7554988	0.84[AMR][1000 genomes]
rs9787149	0.84[AMR][1000 genomes]
rs9787255	0.84[ASW][hapmap];0.85[CEU][hapmap];0.89[GIH][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	nsv523150	chr1:85538947-85541164	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv2763574	chr1:85539127-85542620	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12063120	MCOLN2	cis	multi-tissue	Pritchard
rs12063120	MCOLN2	cis	Thyroid	GTEx
rs12063120	MCOLN2	Cis_1M	lymphoblastoid	RTeQTL
rs12063120	MCOLN2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85529600-85552400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:85539600-85541400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:85539800-85541000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:85540000-85540600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:85540200-85554400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links