Variant report

Variant	rs12578752
Chromosome Location	chr12:66565689-66565690
allele	C/T
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	POLR2A	chr12:66565592-66565734	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:66537187..66538764-chr12:66565485..66567103,2	K562	blood:
2	chr12:66530596..66534894-chr12:66562580..66565717,4	K562	blood:
3	chr12:66564516..66566525-chr12:66607365..66609026,2	K562	blood:
4	chr12:66564277..66567051-chr12:66577014..66579195,2	MCF-7	breast:
5	chr12:66535914..66538687-chr12:66565341..66566985,2	K562	blood:

Variant related genes	Relation type
ENSG00000228144	TF binding region
TMBIM4	TF binding region
ENSG00000155957	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10459263	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs10506475	0.93[EUR][1000 genomes]
rs10506479	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10878379	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs10878380	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs10878384	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs10878387	0.93[EUR][1000 genomes]
rs10878388	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs11176040	0.92[EUR][1000 genomes]
rs11176041	0.93[EUR][1000 genomes]
rs11176042	0.93[EUR][1000 genomes]
rs11176044	0.93[EUR][1000 genomes]
rs11176046	0.93[EUR][1000 genomes]
rs11176047	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs11176048	0.93[EUR][1000 genomes]
rs11176050	0.93[EUR][1000 genomes]
rs11176051	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs11176058	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs11176059	0.93[EUR][1000 genomes]
rs11176061	0.93[EUR][1000 genomes]
rs11176062	0.93[EUR][1000 genomes]
rs1168736	0.99[ASN][1000 genomes]
rs1168739	0.99[ASN][1000 genomes]
rs1168744	1.00[ASN][1000 genomes]
rs1168757	0.83[ASN][1000 genomes]
rs1168758	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1168772	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1179914	0.99[ASN][1000 genomes]
rs12230221	0.93[EUR][1000 genomes]
rs12230240	0.89[EUR][1000 genomes]
rs12230800	0.82[CEU][hapmap];0.93[EUR][1000 genomes]
rs12306484	0.90[ASN][1000 genomes]
rs12423372	0.85[CEU][hapmap]
rs12426813	0.83[EUR][1000 genomes]
rs12578364	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12578754	0.83[EUR][1000 genomes]
rs12578801	0.85[CEU][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12578994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12581033	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs12581836	0.93[EUR][1000 genomes]
rs12582384	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs12814331	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12814606	0.82[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821415	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12822410	0.92[EUR][1000 genomes]
rs12823414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12823732	0.93[EUR][1000 genomes]
rs12825992	0.93[EUR][1000 genomes]
rs1370129	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs1625441	0.82[ASN][1000 genomes]
rs17245364	0.85[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732893	0.90[ASN][1000 genomes]
rs17825931	0.90[ASN][1000 genomes]
rs17825943	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1797410	0.97[ASN][1000 genomes]
rs1921080	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs1921082	0.95[ASN][1000 genomes]
rs2576183	0.83[ASN][1000 genomes]
rs2701644	0.90[ASN][1000 genomes]
rs2701645	0.90[ASN][1000 genomes]
rs2701653	0.82[ASN][1000 genomes]
rs2701654	0.83[ASN][1000 genomes]
rs2701655	0.84[ASN][1000 genomes]
rs2870786	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs2904498	0.93[EUR][1000 genomes]
rs2917598	0.90[ASN][1000 genomes]
rs34406211	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34552143	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34750837	0.82[EUR][1000 genomes]
rs35085853	0.80[EUR][1000 genomes]
rs35131575	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35187440	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35447479	0.93[EUR][1000 genomes]
rs35971570	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36073795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4281516	0.93[EUR][1000 genomes]
rs59112451	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60102429	0.91[EUR][1000 genomes]
rs66767092	0.93[EUR][1000 genomes]
rs71450848	0.93[EUR][1000 genomes]
rs73315943	0.83[EUR][1000 genomes]
rs737614	0.85[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv1999399	chr12:66565689-66565690	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12578752	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66563800-66567200	Weak transcription	Spleen	Spleen
2	chr12:66564400-66568000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr12:66564400-66569200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:66564400-66570000	Weak transcription	Adipose Nuclei	Adipose
5	chr12:66564800-66566200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr12:66564800-66566200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:66564800-66566200	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr12:66564800-66566600	Weak transcription	Primary B cells from cord blood	blood
9	chr12:66565200-66566200	Enhancers	Primary neutrophils fromperipheralblood	blood

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