Variant report

Variant	rs2870786
Chromosome Location	chr12:66519743-66519744
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:66517857..66521080-chr12:66522803..66525691,6	MCF-7	breast:
2	chr12:66517556..66521125-chr12:66522874..66526131,5	K562	blood:
3	chr12:66510691..66513210-chr12:66517209..66519809,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139233	Chromatin interaction
ENSG00000239335	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10459263	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878379	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878380	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878387	0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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]
rs11176050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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]
rs1168744	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs1168758	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs1168771	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs1168772	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs1179914	0.89[CEU][hapmap]
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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12306484	0.89[CEU][hapmap]
rs12423372	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs12426813	0.90[EUR][1000 genomes]
rs12578364	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12578752	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs12578754	0.90[EUR][1000 genomes]
rs12578801	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[AMR][1000 genomes]
rs12578994	0.89[CEU][hapmap];0.83[CHB][hapmap];0.93[EUR][1000 genomes]
rs12581033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12581836	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12582384	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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	1.00[CEU][hapmap];0.85[YRI][hapmap];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[CEU][hapmap];0.95[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]
rs1370129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1625441	0.89[CEU][hapmap]
rs17245364	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1732893	0.89[CEU][hapmap]
rs17825931	0.81[CHB][hapmap]
rs17825943	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1921080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1921082	0.89[CEU][hapmap]
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	1.00[CEU][hapmap];0.83[CHB][hapmap];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
rs2870786	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	chr12:66509000-66519800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:66509000-66523800	Weak transcription	Pancreas	Pancrea
3	chr12:66509200-66523600	Weak transcription	Gastric	stomach
4	chr12:66512000-66522200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:66513600-66522400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:66513600-66522600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:66513600-66522600	Strong transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:66513600-66523400	Weak transcription	Small Intestine	intestine
9	chr12:66513600-66523800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:66513800-66521000	Strong transcription	Dnd41	blood
11	chr12:66513800-66522400	Strong transcription	Fetal Thymus	thymus
12	chr12:66513800-66522600	Strong transcription	Adipose Nuclei	Adipose
13	chr12:66514000-66522400	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr12:66514000-66522600	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:66514000-66522600	Strong transcription	Fetal Muscle Leg	muscle
16	chr12:66514200-66519800	Strong transcription	HSMM	muscle
17	chr12:66514200-66521200	Strong transcription	Primary T cells from cord blood	blood
18	chr12:66514200-66521400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr12:66514200-66522600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr12:66514200-66522600	Strong transcription	NHDF-Ad	bronchial
21	chr12:66514200-66523200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:66514400-66520600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr12:66514400-66523800	Weak transcription	Spleen	Spleen
24	chr12:66514600-66519800	Strong transcription	Fetal Muscle Trunk	muscle
25	chr12:66514600-66521600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:66514600-66522000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:66514600-66522000	Strong transcription	A549	lung
28	chr12:66514600-66522400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr12:66514600-66522600	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr12:66514600-66522600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr12:66514600-66522600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:66514600-66522600	Strong transcription	Fetal Lung	lung
33	chr12:66514600-66522600	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr12:66514600-66522800	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr12:66514800-66522600	Strong transcription	Fetal Intestine Large	intestine
36	chr12:66515400-66522400	Strong transcription	Liver	Liver
37	chr12:66515400-66522600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:66515400-66522600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr12:66515400-66522600	Strong transcription	Duodenum Mucosa	Duodenum
40	chr12:66515600-66521200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:66515600-66521800	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr12:66515600-66522200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:66515600-66522400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr12:66515600-66523000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr12:66515600-66523600	Weak transcription	Lung	lung
46	chr12:66515800-66521000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:66515800-66521800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:66515800-66522400	Strong transcription	Hela-S3	cervix
49	chr12:66515800-66522400	Strong transcription	HMEC	breast
50	chr12:66515800-66522600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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