Variant report

Variant	rs2289134
Chromosome Location	chr12:66598687-66598688
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	chr12:66561052..66563849-chr12:66595692..66600128,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155957	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10506480	0.81[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs11465955	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11465970	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1179917	0.81[EUR][1000 genomes]
rs17767286	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17767298	0.86[CEU][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1821777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1882200	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2293657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3782347	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4762087	0.90[EUR][1000 genomes]
rs4762088	0.86[CEU][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55715236	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55913894	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56156535	0.90[EUR][1000 genomes]
rs56365678	0.82[EUR][1000 genomes]
rs61927088	0.88[EUR][1000 genomes]
rs61927090	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7302556	0.80[CEU][hapmap];0.88[TSI][hapmap];0.83[EUR][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	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1049537	chr12:66403269-66606174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv899216	chr12:66563835-66716844	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv541517	chr12:66576953-66639823	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2289134	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL
rs2289134	MDM1	cis	parietal	SCAN
rs2289134	TMBIM4	cis	parietal	SCAN
rs2289134	TMBIM4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66583800-66623400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:66589400-66606000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:66589600-66623400	Weak transcription	Spleen	Spleen
4	chr12:66592200-66604400	Weak transcription	NHDF-Ad	bronchial
5	chr12:66592200-66606000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:66592400-66603400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:66592400-66628400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:66593400-66606000	Weak transcription	Adipose Nuclei	Adipose
9	chr12:66593400-66613400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr12:66594400-66598800	Weak transcription	Fetal Lung	lung
11	chr12:66594600-66603800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr12:66597200-66598800	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr12:66597200-66598800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr12:66597200-66603200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr12:66597400-66603200	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr12:66597600-66600800	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr12:66597600-66623400	Weak transcription	Aorta	Aorta
18	chr12:66597800-66601000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:66597800-66609000	Weak transcription	Stomach Mucosa	stomach
20	chr12:66598000-66600800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:66598200-66602000	Strong transcription	Primary hematopoietic stem cells	blood
22	chr12:66598400-66598800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links