Variant report

Variant	rs1168744
Chromosome Location	chr12:66559436-66559437
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:66550852..66561080-chr12:66561565..66565303,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155957	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10459263	0.89[CEU][hapmap];0.87[CHB][hapmap];0.92[GIH][hapmap]
rs10506479	0.82[CHB][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap]
rs10878379	0.80[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap]
rs10878380	0.80[CEU][hapmap]
rs10878384	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs10878388	0.80[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap]
rs11176047	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs11176051	0.80[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap]
rs11176058	0.80[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap]
rs1168736	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168739	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168757	0.93[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1168758	0.89[GIH][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs1168772	0.89[GIH][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs1179914	0.90[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1185253	0.92[EUR][1000 genomes]
rs12230800	0.82[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap]
rs12306484	0.90[CEU][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12423372	0.80[CEU][hapmap]
rs12578364	0.99[ASN][1000 genomes]
rs12578752	1.00[ASN][1000 genomes]
rs12578801	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs12578994	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs12581033	0.80[CEU][hapmap];0.81[CHB][hapmap]
rs12814331	1.00[ASN][1000 genomes]
rs12814606	0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs12823414	0.84[ASN][1000 genomes]
rs12825992	0.85[CEU][hapmap]
rs1370129	0.80[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap]
rs1625441	0.90[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17245364	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs1732893	0.90[CEU][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17825931	0.95[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs17825943	0.94[ASN][1000 genomes]
rs1797404	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs1797410	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1797411	0.80[AFR][1000 genomes]
rs1921080	0.80[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap]
rs1921082	0.90[CEU][hapmap];0.81[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2576183	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2701644	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2701645	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2701653	0.93[GIH][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2701654	0.86[JPT][hapmap];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2701655	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2870786	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs2917598	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34406211	0.92[ASN][1000 genomes]
rs34552143	0.94[ASN][1000 genomes]
rs35131575	0.94[ASN][1000 genomes]
rs35187440	1.00[ASN][1000 genomes]
rs35971570	1.00[ASN][1000 genomes]
rs36073795	1.00[ASN][1000 genomes]
rs57825508	0.81[EUR][1000 genomes]
rs59112451	0.94[ASN][1000 genomes]
rs737614	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1168744	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66525400-66562400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:66525600-66561800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:66536400-66562400	Weak transcription	HMEC	breast
4	chr12:66538600-66560400	Weak transcription	Fetal Brain Male	brain
5	chr12:66539400-66561400	Weak transcription	Fetal Heart	heart
6	chr12:66539400-66562200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:66542800-66563000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:66547400-66562000	Weak transcription	HUVEC	blood vessel
9	chr12:66548400-66562200	Weak transcription	Brain Anterior Caudate	brain
10	chr12:66548600-66562000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr12:66549200-66561800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr12:66549200-66561800	Weak transcription	Right Atrium	heart
13	chr12:66551200-66560400	Weak transcription	HepG2	liver
14	chr12:66553000-66562200	Weak transcription	Brain Angular Gyrus	brain
15	chr12:66553200-66561600	Weak transcription	Colon Smooth Muscle	Colon
16	chr12:66553200-66562400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr12:66553800-66561800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:66554000-66560400	Weak transcription	HSMM	muscle
19	chr12:66554000-66560600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr12:66554000-66560800	Weak transcription	Liver	Liver
21	chr12:66554000-66561000	Weak transcription	Adipose Nuclei	Adipose
22	chr12:66554000-66561200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:66554000-66561800	Weak transcription	HSMMtube	muscle
24	chr12:66554000-66562000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:66554000-66562000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr12:66554000-66562000	Weak transcription	NHEK	skin
27	chr12:66554000-66562000	Weak transcription	Osteobl	bone
28	chr12:66554000-66562200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr12:66554000-66562200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr12:66554000-66562200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr12:66554000-66562200	Weak transcription	NHLF	lung
32	chr12:66554000-66562400	Weak transcription	Brain Germinal Matrix	brain
33	chr12:66554000-66563000	Weak transcription	Gastric	stomach
34	chr12:66554200-66561000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr12:66554200-66562200	Weak transcription	NH-A	brain
36	chr12:66554400-66561000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:66554400-66562000	Weak transcription	Fetal Kidney	kidney
38	chr12:66554600-66560400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr12:66554600-66562000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:66554800-66561800	Weak transcription	Pancreas	Pancrea
41	chr12:66554800-66562200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:66555000-66560800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:66555000-66560800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:66555000-66561600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr12:66555000-66561600	Weak transcription	Lung	lung
46	chr12:66555000-66561800	Weak transcription	Fetal Thymus	thymus
47	chr12:66555000-66562200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:66555000-66562600	Weak transcription	Aorta	Aorta
49	chr12:66555000-66562800	Weak transcription	Esophagus	oesophagus
50	chr12:66555200-66560400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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