Variant report

Variant	rs11176050
Chromosome Location	chr12:66523359-66523360
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:145096186..145098889-chr12:66522673..66525529,2	MCF-7	breast:
2	chr12:66523081..66526604-chr12:66560988..66564576,8	MCF-7	breast:
3	chr12:66523095..66527368-chr12:66532414..66535159,4	MCF-7	breast:
4	chr12:66523311..66525203-chr12:66696051..66697589,2	MCF-7	breast:
5	chr12:66521057..66526734-chr12:66560807..66565257,7	K562	blood:

Variant related genes	Relation type
ENSG00000223380	Chromatin interaction
ENSG00000155957	Chromatin interaction
ENSG00000127311	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10459263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10506475	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10506479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878379	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878380	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176040	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11176041	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11176042	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11176044	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11176046	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11176047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176058	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176059	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168758	0.81[EUR][1000 genomes]
rs1168772	0.81[EUR][1000 genomes]
rs12230221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12230240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12230800	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12426813	0.90[EUR][1000 genomes]
rs12578364	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12578752	0.93[EUR][1000 genomes]
rs12578754	0.90[EUR][1000 genomes]
rs12578801	1.00[AMR][1000 genomes]
rs12578994	0.93[EUR][1000 genomes]
rs12581033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12581836	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12582384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12814331	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12814606	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12821415	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12822410	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12823414	0.85[EUR][1000 genomes]
rs12823732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12825992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17245364	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17825943	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1921080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2870786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2904498	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34406211	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34552143	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35085853	0.84[EUR][1000 genomes]
rs35131575	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35187440	0.93[EUR][1000 genomes]
rs35447479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35971570	0.93[EUR][1000 genomes]
rs36073795	0.93[EUR][1000 genomes]
rs4281516	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57825508	0.88[ASN][1000 genomes]
rs59112451	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60102429	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66767092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71450848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73315943	0.90[EUR][1000 genomes]
rs737614	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11176050	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66509000-66523800	Weak transcription	Pancreas	Pancrea
2	chr12:66509200-66523600	Weak transcription	Gastric	stomach
3	chr12:66513600-66523400	Weak transcription	Small Intestine	intestine
4	chr12:66513600-66523800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:66514400-66523800	Weak transcription	Spleen	Spleen
6	chr12:66515600-66523600	Weak transcription	Lung	lung
7	chr12:66516000-66524000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:66516600-66523800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:66516800-66523600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:66516800-66523600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:66517200-66523400	Weak transcription	Stomach Mucosa	stomach
12	chr12:66518400-66523600	Weak transcription	Right Atrium	heart
13	chr12:66518600-66523400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr12:66518800-66523600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr12:66518800-66523600	Weak transcription	Psoas Muscle	Psoas
16	chr12:66518800-66523600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr12:66519000-66523400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr12:66519000-66523600	Weak transcription	Fetal Kidney	kidney
19	chr12:66519000-66523600	Weak transcription	Right Ventricle	heart
20	chr12:66519000-66523800	Weak transcription	Aorta	Aorta
21	chr12:66519400-66523400	Weak transcription	HSMMtube	muscle
22	chr12:66519600-66523400	Weak transcription	Brain Substantia Nigra	brain
23	chr12:66520000-66523600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr12:66520800-66523400	Weak transcription	Fetal Intestine Small	intestine
25	chr12:66521000-66523400	Enhancers	Fetal Heart	heart
26	chr12:66521400-66523400	Weak transcription	Colonic Mucosa	Colon
27	chr12:66521400-66523800	Weak transcription	Esophagus	oesophagus
28	chr12:66521800-66523400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr12:66521800-66523600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:66522000-66523400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr12:66522000-66523400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr12:66522000-66523600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:66522200-66523400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:66522200-66523400	Weak transcription	Brain Angular Gyrus	brain
35	chr12:66522200-66523400	Enhancers	HepG2	liver
36	chr12:66522400-66523400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:66522400-66523400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr12:66522400-66523400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:66522400-66523400	Weak transcription	Liver	Liver
40	chr12:66522400-66523400	Enhancers	Fetal Brain Male	brain
41	chr12:66522400-66523400	Weak transcription	Fetal Brain Female	brain
42	chr12:66522400-66523400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr12:66522400-66523400	Weak transcription	NH-A	brain
44	chr12:66522400-66523600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:66522400-66523600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr12:66522400-66523600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr12:66522600-66523400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:66522600-66523400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr12:66522600-66523400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr12:66522600-66523400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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