Variant report

Variant	rs12423372
Chromosome Location	chr12:66459480-66459481
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr12:66459422-66460940	ECC-1	luminal epithelium:	n/a	n/a
2	TCF12	chr12:66458556-66460648	SK-N-SH	brain:	n/a	n/a
3	EP300	chr12:66458777-66459493	SK-N-SH	brain:	n/a	chr12:66459143-66459152 chr12:66459144-66459153
4	RUNX3	chr12:66459441-66460923	GM12878	blood:	n/a	n/a
5	GATA3	chr12:66458797-66460570	SK-N-SH	brain:	n/a	chr12:66459273-66459294 chr12:66459411-66459428
6	NFIC	chr12:66458873-66460717	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr12:66458709-66460620	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr12:66459339-66459801	SK-N-MC	brain:	n/a	n/a

Variant related genes	Relation type
RNA5SP362	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10459263	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs10506479	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10878379	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap]
rs10878380	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap]
rs10878384	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs10878388	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs11176047	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs11176051	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs11176058	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs1168744	0.80[CEU][hapmap]
rs1168758	0.80[CEU][hapmap]
rs1168772	0.80[CEU][hapmap]
rs1179914	0.89[CEU][hapmap];0.83[JPT][hapmap]
rs12230800	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs12306484	0.89[CEU][hapmap];0.83[JPT][hapmap]
rs12578752	0.85[CEU][hapmap]
rs12578801	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs12578994	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs12581033	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs12581342	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12581836	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs12582384	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs12814606	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs12817234	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12817410	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12825992	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1370129	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs1625441	0.89[CEU][hapmap]
rs17245364	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs1732893	0.89[CEU][hapmap]
rs1921080	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs1921082	0.89[CEU][hapmap];0.83[JPT][hapmap]
rs2870786	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs35164757	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35515628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35758766	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs737614	1.00[CEU][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv899213	chr12:66389968-66500036	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv832446	chr12:66393863-66501484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12423372	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66453800-66460800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:66454200-66459600	Weak transcription	Fetal Brain Female	brain
3	chr12:66455800-66461200	Enhancers	NHDF-Ad	bronchial
4	chr12:66456000-66460200	Weak transcription	Fetal Kidney	kidney
5	chr12:66456200-66459600	Weak transcription	HepG2	liver
6	chr12:66457200-66460000	Weak transcription	Fetal Muscle Leg	muscle
7	chr12:66457400-66459800	Weak transcription	Fetal Stomach	stomach
8	chr12:66457800-66459600	Enhancers	Osteobl	bone
9	chr12:66457800-66461200	Enhancers	NHLF	lung
10	chr12:66458600-66460600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:66458800-66460400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:66458800-66460800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr12:66458800-66460800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:66458800-66460800	Enhancers	NH-A	brain
15	chr12:66458800-66461200	Enhancers	Primary hematopoietic stem cells	blood
16	chr12:66459000-66459800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:66459000-66460000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:66459000-66460000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:66459400-66459600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:66459400-66459800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:66459400-66460000	Enhancers	GM12878-XiMat	blood
22	chr12:66459400-66460600	Enhancers	Fetal Lung	lung
23	chr12:66459400-66461000	Enhancers	Fetal Brain Male	brain
24	chr12:66459400-66461200	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr12:66459400-66461600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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