Variant report

Variant	rs1168765
Chromosome Location	chr12:66513111-66513112
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:66512970..66515802-chr12:66525883..66527400,2	MCF-7	breast:
2	chr12:66512241..66514451-chr12:66541871..66543985,2	K562	blood:
3	chr12:66510691..66513210-chr12:66517209..66519809,2	MCF-7	breast:
4	chr12:66512047..66516114-chr12:66522625..66525849,5	MCF-7	breast:
5	chr12:66512389..66515308-chr12:66562827..66565112,2	K562	blood:

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

Extended variants
information (count: 29 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10878378	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11176057	0.90[CHB][hapmap];0.87[CHD][hapmap]
rs11176060	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168735	0.92[EUR][1000 genomes]
rs1168754	0.90[CHB][hapmap]
rs1168766	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168770	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1177578	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1183892	0.89[CEU][hapmap];0.98[GIH][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs1184556	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1184884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1185888	0.89[CEU][hapmap];0.98[GIH][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs12823890	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1370126	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1436849	0.82[CEU][hapmap];0.95[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs1732886	0.81[CHB][hapmap]
rs1732887	0.90[CHB][hapmap]
rs1732888	0.90[CHB][hapmap]
rs2576187	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2701652	0.90[CHB][hapmap]
rs2870782	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4296075	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4328252	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7975029	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7979576	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8793	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs1168765	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL
rs1168765	RP11-745O10.2	cis	Esophagus Mucosa	GTEx
rs1168765	TMBIM4	cis	normal skin	skin_eQTL
rs1168765	TMBIM4	cis	parietal	SCAN
rs1168765	RP11-745O10.2	cis	Whole Blood	GTEx
rs1168765	RP11-745O10.2	cis	Heart Left Ventricle	GTEx
rs1168765	TMBIM4	cis	lesional skin	skin_eQTL
rs1168765	RP11-745O10.2	cis	Artery Aorta	GTEx
rs1168765	RP11-745O10.2	cis	Skin Sun Exposed Lower leg	GTEx
rs1168765	TMBIM4	cis	cerebellum	SCAN
rs1168765	RP11-745O10.2	cis	lung	GTEx
rs1168765	TMBIM4	cis	multi-tissue	Pritchard
rs1168765	RP11-745O10.2	cis	Esophagus Muscularis	GTEx
rs1168765	RP11-745O10.2	cis	Stomach	GTEx
rs1168765	FLJ23235	trans	multi-tissue	Pritchard
rs1168765	TMBIM4	cis	uninvolved skin	skin_eQTL
rs1168765	RP11-745O10.2	cis	Thyroid	GTEx
rs1168765	RP11-745O10.2	cis	Artery Tibial	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66501200-66516000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr12:66501400-66514600	Weak transcription	A549	lung
3	chr12:66501400-66515400	Weak transcription	Liver	Liver
4	chr12:66501600-66513200	Weak transcription	Brain Anterior Caudate	brain
5	chr12:66501600-66513200	Weak transcription	HSMM	muscle
6	chr12:66501600-66513600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:66501600-66513800	Weak transcription	Adipose Nuclei	Adipose
8	chr12:66501600-66514600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:66501600-66514600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:66501600-66514600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr12:66501600-66516000	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:66501600-66517600	Weak transcription	Right Ventricle	heart
13	chr12:66501800-66516800	Weak transcription	NHEK	skin
14	chr12:66502000-66513400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:66502000-66518000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:66502400-66515800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:66502400-66516000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr12:66502400-66518400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr12:66502600-66516000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr12:66502600-66516200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:66505400-66516000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:66505800-66514600	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr12:66505800-66515600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:66506400-66514000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr12:66506400-66516400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:66507800-66514600	Weak transcription	Thymus	Thymus
27	chr12:66508600-66515400	Weak transcription	Fetal Brain Female	brain
28	chr12:66509000-66514000	Weak transcription	Fetal Muscle Leg	muscle
29	chr12:66509000-66514400	Weak transcription	Left Ventricle	heart
30	chr12:66509000-66515200	Weak transcription	Lung	lung
31	chr12:66509000-66518200	Weak transcription	Esophagus	oesophagus
32	chr12:66509000-66519800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:66509000-66523800	Weak transcription	Pancreas	Pancrea
34	chr12:66509200-66513800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:66509200-66515800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr12:66509200-66523600	Weak transcription	Gastric	stomach
37	chr12:66509600-66513400	Weak transcription	Primary B cells from cord blood	blood
38	chr12:66509600-66518000	Weak transcription	Ovary	ovary
39	chr12:66509800-66513400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr12:66510000-66513600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr12:66510000-66514400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr12:66510000-66514600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:66510000-66514600	Weak transcription	Fetal Muscle Trunk	muscle
44	chr12:66510200-66513200	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr12:66510600-66513800	Weak transcription	Fetal Thymus	thymus
46	chr12:66510600-66513800	Weak transcription	Dnd41	blood
47	chr12:66510600-66515800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:66511000-66516000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:66511200-66515600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr12:66511400-66513200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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