Variant report

Variant	rs1168772
Chromosome Location	chr12:66590481-66590482
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:66563078..66564733-chr12:66588492..66590792,2	MCF-7	breast:
2	chr12:66583600..66585977-chr12:66589320..66590902,2	MCF-7	breast:
3	chr12:66562116..66564861-chr12:66589137..66592515,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155957	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10459263	0.80[CEU][hapmap];0.96[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs10506475	0.81[EUR][1000 genomes]
rs10506479	0.80[CEU][hapmap];0.96[GIH][hapmap];0.81[EUR][1000 genomes]
rs10878379	0.80[CEU][hapmap];0.96[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs10878380	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs10878384	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs10878387	0.81[EUR][1000 genomes]
rs10878388	0.80[CEU][hapmap];0.96[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs11176041	0.81[EUR][1000 genomes]
rs11176042	0.81[EUR][1000 genomes]
rs11176044	0.81[EUR][1000 genomes]
rs11176046	0.81[EUR][1000 genomes]
rs11176047	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs11176048	0.81[EUR][1000 genomes]
rs11176050	0.81[EUR][1000 genomes]
rs11176051	0.80[CEU][hapmap];0.96[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs11176058	0.80[CEU][hapmap];0.96[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs11176059	0.81[EUR][1000 genomes]
rs11176061	0.81[EUR][1000 genomes]
rs11176062	0.81[EUR][1000 genomes]
rs1152884	1.00[ASW][hapmap];0.89[CEU][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1152888	0.81[CEU][hapmap]
rs1152910	0.88[AFR][1000 genomes]
rs1168736	0.83[ASN][1000 genomes]
rs1168739	0.83[ASN][1000 genomes]
rs1168744	0.89[GIH][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs1168757	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168758	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168760	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs1168773	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs1179914	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs1185253	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1185630	0.86[CHB][hapmap]
rs12230221	0.81[EUR][1000 genomes]
rs12230800	0.96[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs12306484	0.81[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs12423372	0.80[CEU][hapmap]
rs12578364	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12578752	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12578801	0.80[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs12578994	0.81[CHB][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12581033	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs12581836	0.80[CHB][hapmap];0.81[EUR][1000 genomes]
rs12582384	0.81[EUR][1000 genomes]
rs12814331	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12814606	0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12823414	0.86[CHB][hapmap];0.81[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12823732	0.81[EUR][1000 genomes]
rs12825992	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs1370129	0.80[CEU][hapmap];0.96[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs1617632	0.82[MKK][hapmap]
rs1625441	0.86[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs17245364	0.80[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1732875	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1732893	0.93[GIH][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs17825943	0.86[EUR][1000 genomes]
rs1797400	0.95[AFR][1000 genomes]
rs1797401	0.95[AFR][1000 genomes]
rs1797404	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs1797410	0.84[ASN][1000 genomes]
rs1921080	0.80[CEU][hapmap];0.96[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs1921082	0.93[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs2576183	0.96[ASN][1000 genomes]
rs2701644	0.88[ASN][1000 genomes]
rs2701645	0.88[ASN][1000 genomes]
rs2701653	0.86[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2701654	0.86[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2701655	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2870786	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs2904498	0.81[EUR][1000 genomes]
rs2917598	0.88[ASN][1000 genomes]
rs34406211	0.86[EUR][1000 genomes]
rs34552143	0.84[EUR][1000 genomes]
rs35131575	0.86[EUR][1000 genomes]
rs35187440	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35447479	0.81[EUR][1000 genomes]
rs35971570	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36073795	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4281516	0.81[EUR][1000 genomes]
rs59112451	0.86[EUR][1000 genomes]
rs66767092	0.81[EUR][1000 genomes]
rs71450848	0.81[EUR][1000 genomes]
rs737614	0.80[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][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	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	nsv541516	chr12:66547969-66596036	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv899215	chr12:66556960-66594134	Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	n/a
6	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
7	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1168772	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66583600-66591400	Weak transcription	Osteobl	bone
2	chr12:66583800-66593000	Weak transcription	Aorta	Aorta
3	chr12:66583800-66623400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:66585000-66591000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr12:66585000-66591400	Weak transcription	Colon Smooth Muscle	Colon
6	chr12:66585600-66590800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:66585600-66592000	Weak transcription	Right Atrium	heart
8	chr12:66587400-66591800	Enhancers	Primary B cells from cord blood	blood
9	chr12:66588800-66591400	Enhancers	Stomach Mucosa	stomach
10	chr12:66589200-66591400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:66589400-66590600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr12:66589400-66591400	Weak transcription	Right Ventricle	heart
13	chr12:66589400-66591800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:66589400-66593200	Weak transcription	Left Ventricle	heart
15	chr12:66589400-66606000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:66589600-66591000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr12:66589600-66591200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:66589600-66623400	Weak transcription	Spleen	Spleen
19	chr12:66589800-66590600	Enhancers	Adipose Nuclei	Adipose
20	chr12:66589800-66592400	Enhancers	HUVEC	blood vessel
21	chr12:66590000-66591000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:66590000-66591200	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr12:66590000-66591400	Enhancers	Fetal Lung	lung
24	chr12:66590200-66591000	Enhancers	Primary B cells from peripheral blood	blood
25	chr12:66590200-66591200	Flanking Active TSS	GM12878-XiMat	blood
26	chr12:66590200-66591200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr12:66590200-66591800	Enhancers	Fetal Kidney	kidney
28	chr12:66590200-66592200	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr12:66590200-66592200	Enhancers	NHDF-Ad	bronchial
30	chr12:66590200-66592400	Enhancers	H1 Cell Line	embryonic stem cell
31	chr12:66590200-66592400	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr12:66590200-66592400	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr12:66590400-66590600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:66590400-66590800	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr12:66590400-66590800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:66590400-66591400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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