Variant report

Variant	rs11176054
Chromosome Location	chr12:66531603-66531604
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:66529650..66532056-chr12:66539532..66541211,2	MCF-7	breast:
2	chr12:66524156..66526872-chr12:66529144..66534313,4	K562	blood:
3	chr12:66530596..66534894-chr12:66562580..66565717,4	K562	blood:

Variant related genes	Relation type
ENSG00000139233	Chromatin interaction
ENSG00000155957	Chromatin interaction
ENSG00000239335	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10400539	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506478	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10878381	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10878382	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10878383	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10878389	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10878391	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11176043	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11176056	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11176063	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176065	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11176067	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11176068	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11176080	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11176082	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12227630	0.85[EUR][1000 genomes]
rs12832926	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17767200	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1882201	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1898304	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1921083	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2141709	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2178486	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2870781	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34645929	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34755483	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4296075	0.80[AMR][1000 genomes]
rs4474482	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4575321	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56271210	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7295147	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7302893	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7305938	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7966453	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7966561	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7979029	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7979775	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11176054	RP11-745O10.2	cis	Artery Tibial	GTEx
rs11176054	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL
rs11176054	RP11-745O10.2	cis	lung	GTEx
rs11176054	RP11-745O10.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11176054	RP11-745O10.2	cis	Whole Blood	GTEx
rs11176054	RP11-745O10.2	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66525000-66533200	Weak transcription	Gastric	stomach
2	chr12:66525200-66533200	Weak transcription	Esophagus	oesophagus
3	chr12:66525200-66533200	Weak transcription	Pancreas	Pancrea
4	chr12:66525200-66534400	Weak transcription	Small Intestine	intestine
5	chr12:66525400-66533200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr12:66525400-66533200	Weak transcription	Spleen	Spleen
7	chr12:66525400-66533400	Weak transcription	Aorta	Aorta
8	chr12:66525400-66533400	Weak transcription	Fetal Brain Male	brain
9	chr12:66525400-66534400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:66525400-66562400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:66525600-66531800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr12:66525600-66533200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr12:66525600-66533400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:66525600-66533400	Weak transcription	Brain Substantia Nigra	brain
15	chr12:66525600-66533600	Weak transcription	Right Ventricle	heart
16	chr12:66525600-66536000	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:66525600-66536400	Weak transcription	Stomach Mucosa	stomach
18	chr12:66525600-66549000	Weak transcription	Colonic Mucosa	Colon
19	chr12:66525600-66552400	Weak transcription	Brain Angular Gyrus	brain
20	chr12:66525600-66561800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:66525800-66532400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr12:66525800-66533400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr12:66526000-66533400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr12:66526200-66534200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:66526400-66533200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr12:66526400-66536000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr12:66526600-66533200	Weak transcription	Fetal Stomach	stomach
28	chr12:66526600-66533200	Weak transcription	Thymus	Thymus
29	chr12:66526600-66534400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr12:66526600-66534400	Weak transcription	HepG2	liver
31	chr12:66526600-66557200	Weak transcription	Psoas Muscle	Psoas
32	chr12:66526800-66533200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr12:66526800-66533200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:66526800-66538600	Weak transcription	Hela-S3	cervix
35	chr12:66527000-66531800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:66527000-66531800	Weak transcription	HMEC	breast
37	chr12:66527000-66533200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:66527000-66554400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:66527200-66533200	Weak transcription	Fetal Intestine Small	intestine
40	chr12:66527400-66533200	Weak transcription	Fetal Heart	heart
41	chr12:66529800-66532000	Strong transcription	NHEK	skin
42	chr12:66529800-66532600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr12:66529800-66532800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:66529800-66532800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr12:66529800-66533200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:66529800-66533600	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr12:66530000-66531800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:66530000-66532000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:66530000-66532000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr12:66530000-66532000	Strong transcription	Brain Anterior Caudate	brain

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