Variant report

Variant	rs4964090
Chromosome Location	chr12:64944069-64944070
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:64920914..64922948-chr12:64942008..64944080,2	MCF-7	breast:
2	chr12:64941391..64946313-chr12:65088501..65093456,7	MCF-7	breast:
3	chr12:64942992..64944148-chr12:65089834..65092133,12	K562	blood:
4	chr12:64941758..64945041-chr12:65003195..65005244,3	MCF-7	breast:
5	chr12:64943285..64945893-chr12:65089552..65091064,2	K562	blood:

Variant related genes	Relation type
ENSG00000268028	Chromatin interaction
ENSG00000153179	Chromatin interaction
ENSG00000256670	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10878188	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10878193	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878194	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175431	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11175432	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11175433	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11175436	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11175437	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175438	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175448	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4964109	0.95[JPT][hapmap]
rs4964111	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61933867	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61933868	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61933869	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61933871	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302018	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302385	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7306956	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7312168	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7484351	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7972780	0.95[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832443	chr12:64878856-65057265	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4964090	C12orf56	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64931400-64944800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr12:64939200-64944800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr12:64943000-64946000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:64943400-64944200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:64943400-64946400	Enhancers	Fetal Muscle Leg	muscle
6	chr12:64943600-64944200	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr12:64943600-64944200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:64943600-64946000	Enhancers	Adipose Nuclei	Adipose
9	chr12:64943800-64944600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:64943800-64944800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:64943800-64944800	Weak transcription	Fetal Kidney	kidney
12	chr12:64943800-64945800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:64944000-64944400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:64944000-64944600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:64944000-64946000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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