Variant report

Variant	rs11176056
Chromosome Location	chr12:66533329-66533330
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:66533118-66533746	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr12:66532812-66535172	K562	blood:	n/a	n/a
3	POLR2A	chr12:66533253-66533469	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:66524156..66526872-chr12:66529144..66534313,4	K562	blood:
2	chr12:66530596..66534894-chr12:66562580..66565717,4	K562	blood:
3	chr12:66533040..66534906-chr12:66624306..66626654,2	MCF-7	breast:
4	chr12:66523095..66527368-chr12:66532414..66535159,4	MCF-7	breast:
5	chr12:66524217..66527472-chr12:66531631..66536698,7	K562	blood:
6	chr12:66522934..66525337-chr12:66532980..66535045,5	MCF-7	breast:
7	chr12:66532840..66534600-chr12:66537441..66539657,2	MCF-7	breast:

No data

Variant related genes	Relation type
TMBIM4	TF binding region
ENSG00000155957	Chromatin interaction
ENSG00000139233	Chromatin interaction
ENSG00000239335	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10400539	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10506478	0.92[CEU][hapmap];0.91[CHD][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10735933	0.81[CHB][hapmap]
rs10878381	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878382	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878383	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878389	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10878391	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11176043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11176054	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11176060	0.85[LWK][hapmap];0.86[MKK][hapmap];0.80[AMR][1000 genomes]
rs11176063	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11176065	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176067	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11176068	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11176080	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11176081	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11176082	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12227630	0.85[EUR][1000 genomes]
rs12823890	0.80[AMR][1000 genomes]
rs12832926	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17767200	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882201	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1898304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1921083	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2141709	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2870781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34645929	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34755483	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4296075	0.83[AMR][1000 genomes]
rs4474482	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4575321	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56271210	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61927092	0.83[ASN][1000 genomes]
rs7295147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302893	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7305938	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7966453	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7966561	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7979029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979775	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8793	0.85[LWK][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.80[AMR][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11176056	RP11-745O10.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11176056	TMBIM4	cis	lymphoblastoid	seeQTL
rs11176056	TMBIM4	cis	cerebellum	SCAN
rs11176056	RP11-745O10.2	cis	Whole Blood	GTEx
rs11176056	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL
rs11176056	TMBIM4	cis	parietal	SCAN
rs11176056	RP11-745O10.2	cis	lung	GTEx
rs11176056	RP11-745O10.2	cis	Artery Tibial	GTEx
rs11176056	RP11-745O10.2	cis	Thyroid	GTEx
rs11176056	LLPH	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66525200-66534400	Weak transcription	Small Intestine	intestine
2	chr12:66525400-66533400	Weak transcription	Aorta	Aorta
3	chr12:66525400-66533400	Weak transcription	Fetal Brain Male	brain
4	chr12:66525400-66534400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:66525400-66562400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:66525600-66533400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:66525600-66533400	Weak transcription	Brain Substantia Nigra	brain
8	chr12:66525600-66533600	Weak transcription	Right Ventricle	heart
9	chr12:66525600-66536000	Weak transcription	Brain Hippocampus Middle	brain
10	chr12:66525600-66536400	Weak transcription	Stomach Mucosa	stomach
11	chr12:66525600-66549000	Weak transcription	Colonic Mucosa	Colon
12	chr12:66525600-66552400	Weak transcription	Brain Angular Gyrus	brain
13	chr12:66525600-66561800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr12:66525800-66533400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr12:66526000-66533400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr12:66526200-66534200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:66526400-66536000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:66526600-66534400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:66526600-66534400	Weak transcription	HepG2	liver
20	chr12:66526600-66557200	Weak transcription	Psoas Muscle	Psoas
21	chr12:66526800-66538600	Weak transcription	Hela-S3	cervix
22	chr12:66527000-66554400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:66529800-66533600	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr12:66530000-66533400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr12:66530000-66533400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:66530000-66533400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:66530000-66533400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr12:66530000-66533400	Strong transcription	Osteobl	bone
29	chr12:66530000-66534000	Strong transcription	Duodenum Mucosa	Duodenum
30	chr12:66530000-66534000	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:66530000-66534000	Strong transcription	Fetal Muscle Trunk	muscle
32	chr12:66530000-66534200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:66530000-66534200	Strong transcription	Primary B cells from peripheral blood	blood
34	chr12:66530000-66534200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr12:66530000-66534200	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr12:66530000-66534200	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr12:66530000-66534200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr12:66530000-66534200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:66530000-66534200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:66530000-66534200	Strong transcription	Adipose Nuclei	Adipose
41	chr12:66530000-66534400	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr12:66530000-66534600	Strong transcription	Primary T cells from cord blood	blood
43	chr12:66530000-66534600	Strong transcription	Fetal Thymus	thymus
44	chr12:66530000-66535400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:66530000-66535800	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr12:66530000-66540800	Strong transcription	Placenta	Placenta
47	chr12:66530000-66544000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:66530000-66547200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:66530600-66536000	Strong transcription	HSMM	muscle
50	chr12:66530800-66533400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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