Variant report

Variant	rs60102429
Chromosome Location	chr12:66551171-66551172
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	chr12:66548703..66551216-chr12:66555058..66558052,2	MCF-7	breast:
2	chr12:66550852..66561080-chr12:66561565..66565303,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155957	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10459263	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10506475	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10506479	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878379	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10878380	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10878384	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878387	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878388	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176040	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11176041	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11176042	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11176044	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11176046	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11176047	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11176048	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11176050	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11176051	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176058	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176059	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176061	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176062	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12230221	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12230240	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12230800	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12426813	0.88[EUR][1000 genomes]
rs12578364	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12578752	0.91[EUR][1000 genomes]
rs12578754	0.88[EUR][1000 genomes]
rs12578801	1.00[AMR][1000 genomes]
rs12578994	0.91[EUR][1000 genomes]
rs12581033	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12581836	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12582384	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12814331	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12814606	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12821415	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12822410	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12823414	0.84[EUR][1000 genomes]
rs12823732	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12825992	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1370129	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17245364	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17825943	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1921080	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2870786	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2904498	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34406211	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34552143	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35085853	0.82[EUR][1000 genomes]
rs35131575	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35187440	0.91[EUR][1000 genomes]
rs35447479	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35971570	0.91[EUR][1000 genomes]
rs36073795	0.91[EUR][1000 genomes]
rs4281516	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57825508	0.86[ASN][1000 genomes]
rs59112451	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66767092	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71450848	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73315943	0.88[EUR][1000 genomes]
rs737614	0.91[EUR][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
rs60102429	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 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	chr12:66525600-66552400	Weak transcription	Brain Angular Gyrus	brain
3	chr12:66525600-66561800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:66526600-66557200	Weak transcription	Psoas Muscle	Psoas
5	chr12:66527000-66554400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:66533800-66553000	Weak transcription	Aorta	Aorta
7	chr12:66533800-66553000	Weak transcription	Spleen	Spleen
8	chr12:66533800-66553800	Weak transcription	Esophagus	oesophagus
9	chr12:66533800-66554400	Weak transcription	Lung	lung
10	chr12:66534600-66555600	Weak transcription	Small Intestine	intestine
11	chr12:66534800-66552800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:66536200-66553600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:66536200-66558000	Weak transcription	Fetal Brain Female	brain
14	chr12:66536400-66552800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:66536400-66553000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:66536400-66556200	Weak transcription	Right Ventricle	heart
17	chr12:66536400-66557600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:66536400-66562400	Weak transcription	HMEC	breast
19	chr12:66536800-66552800	Weak transcription	HSMMtube	muscle
20	chr12:66536800-66556200	Weak transcription	Left Ventricle	heart
21	chr12:66537200-66553000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr12:66537400-66552400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:66537400-66556200	Weak transcription	Ovary	ovary
24	chr12:66537600-66552600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr12:66538400-66552800	Weak transcription	Fetal Kidney	kidney
26	chr12:66538400-66556200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr12:66538600-66560400	Weak transcription	Fetal Brain Male	brain
28	chr12:66539000-66552800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:66539000-66553400	Weak transcription	NH-A	brain
30	chr12:66539200-66552800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:66539200-66558400	Weak transcription	A549	lung
32	chr12:66539400-66556200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr12:66539400-66561400	Weak transcription	Fetal Heart	heart
34	chr12:66539400-66562200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:66541600-66553600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:66542600-66552800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:66542800-66552800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr12:66542800-66563000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr12:66543000-66552800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr12:66543200-66552800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr12:66543600-66553000	Weak transcription	Adipose Nuclei	Adipose
42	chr12:66544000-66552800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr12:66544200-66553000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr12:66544200-66557600	Weak transcription	K562	blood
45	chr12:66544600-66552600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr12:66544600-66552600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:66544600-66552800	Weak transcription	Thymus	Thymus
48	chr12:66544600-66553400	Weak transcription	Fetal Lung	lung
49	chr12:66544800-66552800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:66544800-66552800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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