Variant report

Variant	rs1625441
Chromosome Location	chr12:66585129-66585130
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:66575489..66578360-chr12:66583089..66585352,2	K562	blood:
2	chr12:66583600..66585977-chr12:66589320..66590902,2	MCF-7	breast:
3	chr12:66578489..66581069-chr12:66583580..66586870,3	K562	blood:
4	chr12:66570661..66572865-chr12:66583805..66585652,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10459263	0.89[CEU][hapmap];0.92[GIH][hapmap]
rs10506479	0.89[CEU][hapmap];0.93[GIH][hapmap]
rs10878379	0.89[CEU][hapmap];0.93[GIH][hapmap]
rs10878380	0.89[CEU][hapmap]
rs10878384	0.89[CEU][hapmap]
rs10878388	0.89[CEU][hapmap];0.93[GIH][hapmap]
rs11176047	0.89[CEU][hapmap]
rs11176051	0.89[CEU][hapmap];0.93[GIH][hapmap]
rs11176058	0.89[CEU][hapmap];0.93[GIH][hapmap]
rs1152888	1.00[MEX][hapmap];0.83[TSI][hapmap]
rs1168736	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1168739	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1168744	0.90[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1168757	0.83[ASW][hapmap];0.81[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1168758	0.86[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1168760	0.82[CHB][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1168761	0.82[AMR][1000 genomes]
rs1168772	0.86[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1179914	1.00[CEU][hapmap];0.91[JPT][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1185253	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1185630	0.82[CHB][hapmap];0.82[AMR][1000 genomes]
rs12230800	0.88[CEU][hapmap];0.93[GIH][hapmap]
rs12306484	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12423372	0.89[CEU][hapmap]
rs12578364	0.82[ASN][1000 genomes]
rs12578752	0.82[ASN][1000 genomes]
rs12578801	0.89[CEU][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap]
rs12578994	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12581033	0.89[CEU][hapmap]
rs12582384	0.88[CEU][hapmap]
rs12814331	0.82[ASN][1000 genomes]
rs12814606	0.88[CEU][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs12823414	0.81[JPT][hapmap];0.96[ASN][1000 genomes]
rs12825992	1.00[CEU][hapmap]
rs1370129	0.89[CEU][hapmap];0.93[GIH][hapmap]
rs17245364	0.89[CEU][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1732875	0.90[ASN][1000 genomes]
rs1732893	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17825931	0.83[JPT][hapmap]
rs1797404	0.81[CEU][hapmap];0.95[CHD][hapmap];0.82[LWK][hapmap];0.85[ASN][1000 genomes]
rs1797410	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1921080	0.89[CEU][hapmap];0.93[GIH][hapmap]
rs1921082	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2576183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2701644	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2701645	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2701653	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2701654	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2701655	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2870786	0.89[CEU][hapmap]
rs2917598	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35187440	0.82[ASN][1000 genomes]
rs35971570	0.82[ASN][1000 genomes]
rs36073795	0.82[ASN][1000 genomes]
rs737614	0.89[CEU][hapmap];0.91[JPT][hapmap];0.82[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
rs1625441	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66582400-66585400	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr12:66582400-66586000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:66583400-66585200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:66583400-66585600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:66583400-66586000	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr12:66583600-66585200	Weak transcription	Spleen	Spleen
7	chr12:66583600-66585400	Weak transcription	Esophagus	oesophagus
8	chr12:66583600-66585400	Weak transcription	Ovary	ovary
9	chr12:66583600-66585600	Enhancers	Brain Germinal Matrix	brain
10	chr12:66583600-66585800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr12:66583600-66589000	Weak transcription	Brain Substantia Nigra	brain
12	chr12:66583600-66589000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr12:66583600-66591400	Weak transcription	Osteobl	bone
14	chr12:66583800-66589000	Weak transcription	Placenta	Placenta
15	chr12:66583800-66593000	Weak transcription	Aorta	Aorta
16	chr12:66583800-66623400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:66584200-66585600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr12:66584200-66585600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:66584200-66586000	Active TSS	Primary B cells from cord blood	blood
20	chr12:66584400-66585400	Enhancers	HUVEC	blood vessel
21	chr12:66584400-66585600	Enhancers	Fetal Muscle Leg	muscle
22	chr12:66584400-66585800	Flanking Active TSS	Fetal Lung	lung
23	chr12:66584400-66588800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr12:66584600-66585600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:66584600-66585600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
26	chr12:66584600-66585800	Flanking Active TSS	GM12878-XiMat	blood
27	chr12:66584600-66586000	Enhancers	Gastric	stomach
28	chr12:66584600-66586000	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr12:66584600-66586400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr12:66584800-66585600	Enhancers	Left Ventricle	heart
31	chr12:66584800-66585600	Enhancers	Lung	lung
32	chr12:66584800-66585600	Enhancers	Right Atrium	heart
33	chr12:66585000-66585200	Bivalent Enhancer	Brain Anterior Caudate	brain
34	chr12:66585000-66585200	Enhancers	Right Ventricle	heart
35	chr12:66585000-66585600	Enhancers	Adipose Nuclei	Adipose
36	chr12:66585000-66585800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:66585000-66585800	Enhancers	Fetal Kidney	kidney
38	chr12:66585000-66586000	Enhancers	Stomach Mucosa	stomach
39	chr12:66585000-66590000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:66585000-66591000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr12:66585000-66591400	Weak transcription	Colon Smooth Muscle	Colon

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