Variant report

Variant	rs12823414
Chromosome Location	chr12:66592025-66592026
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	chr12:66588124..66590296-chr12:66590579..66593345,2	K562	blood:
2	chr12:66562116..66564861-chr12:66589137..66592515,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155957	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10459263	0.85[EUR][1000 genomes]
rs10506475	0.85[EUR][1000 genomes]
rs10506479	0.85[EUR][1000 genomes]
rs10878379	0.85[EUR][1000 genomes]
rs10878380	0.85[EUR][1000 genomes]
rs10878384	0.85[EUR][1000 genomes]
rs10878387	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs10878388	0.85[EUR][1000 genomes]
rs11176040	0.84[EUR][1000 genomes]
rs11176041	0.85[EUR][1000 genomes]
rs11176042	0.85[EUR][1000 genomes]
rs11176044	0.85[EUR][1000 genomes]
rs11176046	0.85[EUR][1000 genomes]
rs11176047	0.85[EUR][1000 genomes]
rs11176048	0.85[EUR][1000 genomes]
rs11176050	0.85[EUR][1000 genomes]
rs11176051	0.85[EUR][1000 genomes]
rs11176058	0.85[EUR][1000 genomes]
rs11176059	0.85[EUR][1000 genomes]
rs11176061	0.85[EUR][1000 genomes]
rs11176062	0.85[EUR][1000 genomes]
rs1168736	0.83[ASN][1000 genomes]
rs1168739	0.83[ASN][1000 genomes]
rs1168744	0.84[ASN][1000 genomes]
rs1168757	0.86[CHB][hapmap];0.81[JPT][hapmap];0.99[ASN][1000 genomes]
rs1168758	0.86[CHB][hapmap];0.81[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168772	0.86[CHB][hapmap];0.81[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1179914	0.83[ASN][1000 genomes]
rs1185253	0.94[ASN][1000 genomes]
rs12230221	0.85[EUR][1000 genomes]
rs12230240	0.81[EUR][1000 genomes]
rs12230800	0.85[EUR][1000 genomes]
rs12306484	0.88[ASN][1000 genomes]
rs12578364	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12578752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12578801	0.81[ASN][1000 genomes]
rs12578994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12581033	0.85[EUR][1000 genomes]
rs12581836	0.85[EUR][1000 genomes]
rs12582384	0.85[EUR][1000 genomes]
rs12814331	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12814606	0.84[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12821415	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12822410	0.84[EUR][1000 genomes]
rs12823732	0.85[EUR][1000 genomes]
rs12825992	0.85[EUR][1000 genomes]
rs1370129	0.85[EUR][1000 genomes]
rs1625441	0.81[JPT][hapmap];0.96[ASN][1000 genomes]
rs17245364	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1732875	0.93[ASN][1000 genomes]
rs1732893	0.84[ASN][1000 genomes]
rs17825943	0.90[EUR][1000 genomes]
rs1797404	0.81[ASN][1000 genomes]
rs1797410	0.84[ASN][1000 genomes]
rs1921080	0.85[EUR][1000 genomes]
rs1921082	0.84[ASN][1000 genomes]
rs2576183	0.96[ASN][1000 genomes]
rs2701644	0.88[ASN][1000 genomes]
rs2701645	0.88[ASN][1000 genomes]
rs2701653	0.81[JPT][hapmap];0.96[ASN][1000 genomes]
rs2701654	0.81[JPT][hapmap];0.96[ASN][1000 genomes]
rs2701655	1.00[ASN][1000 genomes]
rs2870786	0.85[EUR][1000 genomes]
rs2904498	0.85[EUR][1000 genomes]
rs2917598	0.88[ASN][1000 genomes]
rs34406211	0.90[EUR][1000 genomes]
rs34552143	0.89[EUR][1000 genomes]
rs35131575	0.90[EUR][1000 genomes]
rs35187440	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35447479	0.85[EUR][1000 genomes]
rs35971570	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36073795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4281516	0.85[EUR][1000 genomes]
rs59112451	0.90[EUR][1000 genomes]
rs60102429	0.84[EUR][1000 genomes]
rs66767092	0.85[EUR][1000 genomes]
rs71450848	0.85[EUR][1000 genomes]
rs737614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
5	nsv899215	chr12:66556960-66594134	Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	n/a
6	nsv899216	chr12:66563835-66716844	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv541517	chr12:66576953-66639823	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12823414	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66583800-66593000	Weak transcription	Aorta	Aorta
2	chr12:66583800-66623400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:66589400-66593200	Weak transcription	Left Ventricle	heart
4	chr12:66589400-66606000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:66589600-66623400	Weak transcription	Spleen	Spleen
6	chr12:66589800-66592400	Enhancers	HUVEC	blood vessel
7	chr12:66590200-66592200	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr12:66590200-66592200	Enhancers	NHDF-Ad	bronchial
9	chr12:66590200-66592400	Enhancers	H1 Cell Line	embryonic stem cell
10	chr12:66590200-66592400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr12:66590200-66592400	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr12:66590800-66592200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr12:66590800-66592200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:66590800-66592400	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr12:66591000-66592400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:66591000-66593400	Enhancers	Adipose Nuclei	Adipose
17	chr12:66591000-66593800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr12:66591200-66592200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:66591200-66592200	ZNF genes & repeats	GM12878-XiMat	blood
20	chr12:66591200-66593200	Genic enhancers	Primary monocytes fromperipheralblood	blood
21	chr12:66591400-66592200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
22	chr12:66591400-66592400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr12:66591400-66594000	Genic enhancers	Monocytes-CD14+_RO01746	blood
24	chr12:66591400-66594400	Strong transcription	Primary hematopoietic stem cells	blood
25	chr12:66591400-66597000	Weak transcription	Stomach Mucosa	stomach
26	chr12:66591600-66593400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:66591600-66593800	Weak transcription	NHLF	lung
28	chr12:66591800-66592400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:66591800-66592400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:66591800-66592400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:66591800-66592400	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr12:66592000-66592200	Flanking Active TSS	Fetal Lung	lung
33	chr12:66592000-66592400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr12:66592000-66593200	Weak transcription	Colon Smooth Muscle	Colon
35	chr12:66592000-66593200	Enhancers	Right Atrium	heart

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