Variant report

Variant	rs12579441
Chromosome Location	chr12:105367289-105367290
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105365761..105368091-chr12:105378210..105380629,2	MCF-7	breast:
2	chr12:105350976..105355078-chr12:105366279..105369986,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151131	Chromatin interaction
ENSG00000136052	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11834087	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12579120	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12579129	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12579202	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12579469	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12579790	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12580237	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12580271	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12580282	1.00[EUR][1000 genomes]
rs12580384	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12581352	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12582090	0.82[ASW][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12582132	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12582312	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs17036429	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs17036433	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17036489	0.93[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs17036545	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs17036606	0.86[ASW][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35938519	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4369494	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4545639	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs61060789	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7135496	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73383473	0.87[AMR][1000 genomes]
rs73383478	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73383483	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73383487	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73383495	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73383498	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73387230	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv869	chr12:105363425-105394904	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12579441	C12orf45	cis	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105360400-105368000	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr12:105363600-105368000	Weak transcription	GM12878-XiMat	blood
3	chr12:105365200-105368600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:105365400-105368200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:105365600-105368400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:105365800-105368200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:105365800-105368400	Weak transcription	Osteobl	bone
8	chr12:105365800-105368600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:105365800-105368600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr12:105367000-105368000	Enhancers	NHEK	skin
11	chr12:105367000-105368200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:105367000-105368600	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links