Variant report

Variant	rs60878594
Chromosome Location	chr12:46805262-46805263
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46764723..46767273-chr12:46802452..46805727,3	MCF-7	breast:
2	chr12:46798219..46802284-chr12:46803095..46805948,4	K562	blood:
3	chr12:46775337..46777845-chr12:46804415..46806846,2	K562	blood:
4	chr12:46794174..46798124-chr12:46799495..46805327,7	K562	blood:
5	chr12:46804079..46806251-chr12:46809068..46811105,2	K562	blood:
6	chr12:46660899..46662857-chr12:46803892..46806349,2	MCF-7	breast:
7	chr12:46545129..46547951-chr12:46804730..46806716,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134294	Chromatin interaction
ENSG00000111371	Chromatin interaction
ENSG00000258096	Chromatin interaction
ENSG00000257261	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11183454	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11183467	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11183482	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11183487	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1125908	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11830080	1.00[EUR][1000 genomes]
rs11834905	1.00[AMR][1000 genomes]
rs11837634	1.00[EUR][1000 genomes]
rs12299499	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12317255	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12320438	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12321512	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12321642	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12322378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13377959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17096765	1.00[EUR][1000 genomes]
rs17096793	1.00[EUR][1000 genomes]
rs17096884	1.00[AMR][1000 genomes]
rs17096896	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17096922	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2085682	1.00[EUR][1000 genomes]
rs34280632	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35875247	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36010856	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3742061	1.00[AMR][1000 genomes]
rs56036156	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56160202	1.00[EUR][1000 genomes]
rs56196954	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56314009	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57425661	1.00[AMR][1000 genomes]
rs58460251	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58890669	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59608605	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60565802	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61406609	1.00[AMR][1000 genomes]
rs73282591	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73290315	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74082237	1.00[EUR][1000 genomes]
rs74082254	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74082263	1.00[EUR][1000 genomes]
rs74082274	1.00[EUR][1000 genomes]
rs74083758	1.00[EUR][1000 genomes]
rs7488027	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7954314	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7965618	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7967889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7977319	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs923788	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46795000-46809200	Weak transcription	Esophagus	oesophagus
2	chr12:46797000-46819800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:46797800-46805400	Weak transcription	HepG2	liver
4	chr12:46798600-46807200	Weak transcription	Small Intestine	intestine
5	chr12:46798800-46805800	Weak transcription	Primary B cells from cord blood	blood
6	chr12:46798800-46806800	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:46799000-46809200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:46801000-46808200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:46801200-46805400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:46801800-46805400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:46802000-46812200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:46802800-46807200	Weak transcription	Fetal Lung	lung
13	chr12:46803000-46806800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:46803200-46809400	Weak transcription	Left Ventricle	heart
15	chr12:46804000-46805400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:46804000-46805400	Enhancers	Hela-S3	cervix
17	chr12:46804200-46807400	Weak transcription	HUVEC	blood vessel
18	chr12:46804600-46806400	Weak transcription	Psoas Muscle	Psoas
19	chr12:46804800-46805600	Enhancers	Fetal Heart	heart
20	chr12:46804800-46808600	Weak transcription	Osteobl	bone
21	chr12:46804800-46809400	Weak transcription	Adipose Nuclei	Adipose
22	chr12:46805200-46805600	Enhancers	Fetal Intestine Small	intestine

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