Variant report

Variant	rs59112451
Chromosome Location	chr12:66553000-66553001
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	chr12:66550852..66561080-chr12:66561565..66565303,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155957	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10459263	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10506475	0.95[EUR][1000 genomes]
rs10506479	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10878379	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10878380	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10878384	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10878387	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10878388	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11176040	0.93[EUR][1000 genomes]
rs11176041	0.95[EUR][1000 genomes]
rs11176042	0.95[EUR][1000 genomes]
rs11176044	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11176046	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11176047	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11176048	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11176050	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11176051	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11176058	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11176059	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11176061	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11176062	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1168736	0.93[ASN][1000 genomes]
rs1168739	0.93[ASN][1000 genomes]
rs1168744	0.94[ASN][1000 genomes]
rs1168758	0.86[EUR][1000 genomes]
rs1168772	0.86[EUR][1000 genomes]
rs1179914	0.93[ASN][1000 genomes]
rs12230221	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12230240	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12230800	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12306484	0.84[ASN][1000 genomes]
rs12426813	0.85[EUR][1000 genomes]
rs12578364	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12578752	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12578754	0.85[EUR][1000 genomes]
rs12578801	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12578994	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12581033	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12581836	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12582384	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12814331	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12814606	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12821415	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12822410	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12823414	0.90[EUR][1000 genomes]
rs12823732	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12825992	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1370129	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17245364	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1732893	0.85[ASN][1000 genomes]
rs17825931	0.96[ASN][1000 genomes]
rs17825943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1797410	0.92[ASN][1000 genomes]
rs1921080	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1921082	0.90[ASN][1000 genomes]
rs2701644	0.84[ASN][1000 genomes]
rs2701645	0.84[ASN][1000 genomes]
rs2870786	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2904498	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2917598	0.84[ASN][1000 genomes]
rs34406211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34552143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34750837	0.84[EUR][1000 genomes]
rs35085853	0.82[EUR][1000 genomes]
rs35131575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35187440	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35447479	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35971570	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36073795	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4281516	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60102429	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66767092	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71450848	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73315943	0.85[EUR][1000 genomes]
rs737614	0.98[EUR][1000 genomes];0.94[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	nsv899214	chr12:66516692-66556960	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59112451	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:137 , 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	chr12:66526600-66557200	Weak transcription	Psoas Muscle	Psoas
4	chr12:66527000-66554400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:66533800-66553000	Weak transcription	Aorta	Aorta
6	chr12:66533800-66553000	Weak transcription	Spleen	Spleen
7	chr12:66533800-66553800	Weak transcription	Esophagus	oesophagus
8	chr12:66533800-66554400	Weak transcription	Lung	lung
9	chr12:66534600-66555600	Weak transcription	Small Intestine	intestine
10	chr12:66536200-66553600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:66536200-66558000	Weak transcription	Fetal Brain Female	brain
12	chr12:66536400-66553000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:66536400-66556200	Weak transcription	Right Ventricle	heart
14	chr12:66536400-66557600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:66536400-66562400	Weak transcription	HMEC	breast
16	chr12:66536800-66556200	Weak transcription	Left Ventricle	heart
17	chr12:66537200-66553000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:66537400-66556200	Weak transcription	Ovary	ovary
19	chr12:66538400-66556200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:66538600-66560400	Weak transcription	Fetal Brain Male	brain
21	chr12:66539000-66553400	Weak transcription	NH-A	brain
22	chr12:66539200-66558400	Weak transcription	A549	lung
23	chr12:66539400-66556200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr12:66539400-66561400	Weak transcription	Fetal Heart	heart
25	chr12:66539400-66562200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:66541600-66553600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr12:66542800-66563000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:66543600-66553000	Weak transcription	Adipose Nuclei	Adipose
29	chr12:66544200-66553000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr12:66544200-66557600	Weak transcription	K562	blood
31	chr12:66544600-66553400	Weak transcription	Fetal Lung	lung
32	chr12:66544800-66553000	Weak transcription	Placenta	Placenta
33	chr12:66545400-66553000	Weak transcription	Fetal Stomach	stomach
34	chr12:66545400-66554600	Weak transcription	Pancreas	Pancrea
35	chr12:66545400-66555000	Weak transcription	GM12878-XiMat	blood
36	chr12:66545600-66553000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:66547200-66553000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr12:66547200-66553000	Weak transcription	HSMM	muscle
39	chr12:66547200-66553000	Weak transcription	NHEK	skin
40	chr12:66547400-66562000	Weak transcription	HUVEC	blood vessel
41	chr12:66548200-66553200	Weak transcription	Brain Germinal Matrix	brain
42	chr12:66548400-66553000	Weak transcription	NHLF	lung
43	chr12:66548400-66562200	Weak transcription	Brain Anterior Caudate	brain
44	chr12:66548600-66553000	Weak transcription	Osteobl	bone
45	chr12:66548600-66562000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr12:66549000-66553600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr12:66549200-66553000	Weak transcription	Brain Hippocampus Middle	brain
48	chr12:66549200-66561800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr12:66549200-66561800	Weak transcription	Right Atrium	heart
50	chr12:66550000-66557600	Strong transcription	Primary T cells from cord blood	blood

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