Variant report

Variant	rs12578364
Chromosome Location	chr12:66557146-66557147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:66548703..66551216-chr12:66555058..66558052,2	MCF-7	breast:
2	chr12:66550852..66561080-chr12:66561565..66565303,15	MCF-7	breast:
3	chr12:66556389..66558004-chr12:66572118..66574414,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155957	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10459263	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10506475	0.93[EUR][1000 genomes]
rs10506479	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10878379	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10878380	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10878384	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10878387	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10878388	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11176040	0.92[EUR][1000 genomes]
rs11176041	0.93[EUR][1000 genomes]
rs11176042	0.93[EUR][1000 genomes]
rs11176044	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11176046	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11176047	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11176048	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11176050	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11176051	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11176058	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11176059	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11176061	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11176062	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1168736	0.98[ASN][1000 genomes]
rs1168739	0.98[ASN][1000 genomes]
rs1168744	0.99[ASN][1000 genomes]
rs1168757	0.82[ASN][1000 genomes]
rs1168758	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1168772	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1179914	0.98[ASN][1000 genomes]
rs12230221	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12230240	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12230800	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12306484	0.89[ASN][1000 genomes]
rs12426813	0.83[EUR][1000 genomes]
rs12578752	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12578754	0.83[EUR][1000 genomes]
rs12578801	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12578994	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12581033	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12581836	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12582384	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12814331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12814606	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12821415	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12822410	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12823414	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12823732	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12825992	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1370129	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1625441	0.82[ASN][1000 genomes]
rs17245364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1732893	0.90[ASN][1000 genomes]
rs17825931	0.90[ASN][1000 genomes]
rs17825943	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1797410	0.96[ASN][1000 genomes]
rs1921080	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1921082	0.94[ASN][1000 genomes]
rs2576183	0.82[ASN][1000 genomes]
rs2701644	0.89[ASN][1000 genomes]
rs2701645	0.89[ASN][1000 genomes]
rs2701653	0.82[ASN][1000 genomes]
rs2701654	0.82[ASN][1000 genomes]
rs2701655	0.83[ASN][1000 genomes]
rs2870786	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2904498	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2917598	0.89[ASN][1000 genomes]
rs34406211	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34552143	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34750837	0.82[EUR][1000 genomes]
rs35085853	0.80[EUR][1000 genomes]
rs35131575	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35187440	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35447479	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35971570	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36073795	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4281516	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59112451	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60102429	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66767092	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71450848	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73315943	0.83[EUR][1000 genomes]
rs737614	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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
rs12578364	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 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	chr12:66536200-66558000	Weak transcription	Fetal Brain Female	brain
5	chr12:66536400-66557600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:66536400-66562400	Weak transcription	HMEC	breast
7	chr12:66538600-66560400	Weak transcription	Fetal Brain Male	brain
8	chr12:66539200-66558400	Weak transcription	A549	lung
9	chr12:66539400-66561400	Weak transcription	Fetal Heart	heart
10	chr12:66539400-66562200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:66542800-66563000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:66544200-66557600	Weak transcription	K562	blood
13	chr12:66547400-66562000	Weak transcription	HUVEC	blood vessel
14	chr12:66548400-66562200	Weak transcription	Brain Anterior Caudate	brain
15	chr12:66548600-66562000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr12:66549200-66561800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:66549200-66561800	Weak transcription	Right Atrium	heart
18	chr12:66550000-66557600	Strong transcription	Primary T cells from cord blood	blood
19	chr12:66550200-66557400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr12:66550400-66559200	Weak transcription	Colonic Mucosa	Colon
21	chr12:66551200-66560400	Weak transcription	HepG2	liver
22	chr12:66551400-66558000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr12:66553000-66562200	Weak transcription	Brain Angular Gyrus	brain
24	chr12:66553200-66561600	Weak transcription	Colon Smooth Muscle	Colon
25	chr12:66553200-66562400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr12:66553400-66559000	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:66553600-66557200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr12:66553800-66557200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr12:66553800-66559200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:66553800-66561800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr12:66554000-66558600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr12:66554000-66558600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr12:66554000-66559200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:66554000-66560400	Weak transcription	HSMM	muscle
35	chr12:66554000-66560600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr12:66554000-66560800	Weak transcription	Liver	Liver
37	chr12:66554000-66561000	Weak transcription	Adipose Nuclei	Adipose
38	chr12:66554000-66561200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr12:66554000-66561800	Weak transcription	HSMMtube	muscle
40	chr12:66554000-66562000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:66554000-66562000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr12:66554000-66562000	Weak transcription	NHEK	skin
43	chr12:66554000-66562000	Weak transcription	Osteobl	bone
44	chr12:66554000-66562200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr12:66554000-66562200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr12:66554000-66562200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr12:66554000-66562200	Weak transcription	NHLF	lung
48	chr12:66554000-66562400	Weak transcription	Brain Germinal Matrix	brain
49	chr12:66554000-66563000	Weak transcription	Gastric	stomach
50	chr12:66554200-66557400	Weak transcription	Primary hematopoietic stem cells	blood

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