Variant report

Variant	rs17245364
Chromosome Location	chr12:66562755-66562756
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:66561525..66563608-chr12:66580703..66583177,2	K562	blood:
2	chr12:66523792..66527078-chr12:66561013..66565049,6	MCF-7	breast:
3	chr12:66530596..66534894-chr12:66562580..66565717,4	K562	blood:
4	chr12:66523081..66526604-chr12:66560988..66564576,8	MCF-7	breast:
5	chr12:66521057..66526734-chr12:66560807..66565257,7	K562	blood:
6	chr12:66561184..66563224-chr12:66629023..66631827,2	MCF-7	breast:
7	chr10:88125321..88128301-chr12:66562414..66564569,2	K562	blood:
8	chr12:66523453..66525027-chr12:66562451..66564555,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000139233	Chromatin interaction
ENSG00000090376	Chromatin interaction
ENSG00000266539	Chromatin interaction
ENSG00000155957	Chromatin interaction
ENSG00000239335	Chromatin interaction
ENSG00000182771	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10459263	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10506475	0.93[EUR][1000 genomes]
rs10506479	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10878379	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10878380	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10878384	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10878387	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10878388	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11176040	0.92[EUR][1000 genomes]
rs11176041	0.93[EUR][1000 genomes]
rs11176042	0.93[EUR][1000 genomes]
rs11176044	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11176046	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11176047	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11176048	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11176050	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11176051	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11176058	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11176059	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11176061	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11176062	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1152888	0.80[CHB][hapmap]
rs1168736	0.99[ASN][1000 genomes]
rs1168739	0.99[ASN][1000 genomes]
rs1168744	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs1168757	0.81[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1168758	0.80[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1168772	0.80[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1179914	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12230221	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12230240	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12230800	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12306484	0.89[CEU][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12423372	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs12426813	0.83[EUR][1000 genomes]
rs12578364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12578752	0.85[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12578754	0.83[EUR][1000 genomes]
rs12578801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12578994	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12581033	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12581836	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12582384	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12814331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12814606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821415	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12822410	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12823414	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12823732	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12825992	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1370129	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1625441	0.89[CEU][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1732893	0.89[CEU][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs17825931	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs17825943	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1797410	0.97[ASN][1000 genomes]
rs1921080	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1921082	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2576183	0.83[ASN][1000 genomes]
rs2701644	0.90[ASN][1000 genomes]
rs2701645	0.90[ASN][1000 genomes]
rs2701653	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2701654	0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs2701655	0.84[ASN][1000 genomes]
rs2870786	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2904498	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2917598	0.90[ASN][1000 genomes]
rs34406211	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34552143	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34750837	0.82[EUR][1000 genomes]
rs35085853	0.80[EUR][1000 genomes]
rs35131575	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35187440	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35447479	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35971570	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36073795	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4281516	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59112451	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60102429	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66767092	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71450848	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73315943	0.83[EUR][1000 genomes]
rs737614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17245364	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66542800-66563000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:66554000-66563000	Weak transcription	Gastric	stomach
3	chr12:66555000-66562800	Weak transcription	Esophagus	oesophagus
4	chr12:66557000-66562800	Weak transcription	Ovary	ovary
5	chr12:66558200-66562800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:66559400-66563000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:66561000-66562800	Weak transcription	Placenta	Placenta
8	chr12:66561400-66562800	Enhancers	Small Intestine	intestine
9	chr12:66561600-66562800	Enhancers	Lung	lung
10	chr12:66561600-66563000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr12:66561600-66563000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr12:66561600-66564400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:66561800-66562800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr12:66561800-66562800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:66561800-66563000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:66561800-66563000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:66562000-66562800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr12:66562000-66562800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
19	chr12:66562000-66562800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr12:66562000-66563000	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr12:66562000-66563000	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr12:66562000-66563000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:66562000-66564200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:66562000-66564400	Active TSS	Stomach Smooth Muscle	stomach
25	chr12:66562000-66564400	Active TSS	GM12878-XiMat	blood
26	chr12:66562000-66564400	Active TSS	HSMMtube	muscle
27	chr12:66562200-66562800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:66562200-66562800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr12:66562200-66562800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:66562200-66562800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr12:66562200-66562800	Flanking Active TSS	Dnd41	blood
32	chr12:66562200-66563000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr12:66562200-66563000	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr12:66562200-66563000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:66562200-66563000	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr12:66562200-66563200	Flanking Active TSS	NH-A	brain
37	chr12:66562200-66564200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:66562200-66564400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:66562200-66564400	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr12:66562200-66564400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:66562200-66564400	Active TSS	NHLF	lung
42	chr12:66562200-66564800	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr12:66562400-66562800	Enhancers	H9 Cell Line	embryonic stem cell
44	chr12:66562400-66562800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr12:66562400-66562800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr12:66562400-66562800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:66562400-66562800	Enhancers	Fetal Brain Male	brain
48	chr12:66562400-66562800	Flanking Active TSS	Fetal Intestine Large	intestine
49	chr12:66562400-66562800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr12:66562400-66562800	Flanking Active TSS	Rectal Smooth Muscle	rectum

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