Variant report

Variant	rs1152909
Chromosome Location	chr12:66630654-66630655
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	chr12:66630487-66631193	HL-60	blood:	n/a	n/a
2	ZNF263	chr12:66629699-66631152	HEK293-T-REx	kidney:	n/a	chr12:66629989-66630010 chr12:66629984-66629993
3	SPI1	chr12:66630539-66631203	HL-60	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000266539	TF binding region
RBMS1P1	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1152884	0.82[JPT][hapmap]
rs1152888	0.82[JPT][hapmap]
rs1152906	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1152907	0.81[AMR][1000 genomes]
rs1152908	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168641	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1168642	0.85[EUR][1000 genomes]
rs1168643	0.96[CEU][hapmap];0.83[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1168644	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168647	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1168648	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1168760	0.86[JPT][hapmap]
rs1168762	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1168771	0.84[CEU][hapmap]
rs1185630	0.83[JPT][hapmap]
rs1370127	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1370128	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1623665	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1624395	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1732877	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
4	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
rs1152909	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66615600-66643400	Weak transcription	Stomach Mucosa	stomach
2	chr12:66626600-66633600	Weak transcription	Fetal Lung	lung
3	chr12:66629000-66633200	Weak transcription	Placenta	Placenta
4	chr12:66629400-66630800	Weak transcription	Lung	lung
5	chr12:66629400-66631800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:66629400-66631800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr12:66629400-66636200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:66629400-66637200	Weak transcription	Aorta	Aorta
9	chr12:66629400-66639800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:66629400-66639800	Weak transcription	Spleen	Spleen
11	chr12:66629400-66641800	Weak transcription	Esophagus	oesophagus
12	chr12:66629400-66645000	Weak transcription	Right Ventricle	heart
13	chr12:66629400-66645400	Weak transcription	Gastric	stomach
14	chr12:66629600-66630800	Weak transcription	Right Atrium	heart
15	chr12:66629600-66631200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:66629600-66632000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:66629600-66634000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:66629600-66634200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:66629600-66639200	Weak transcription	Ovary	ovary
20	chr12:66629600-66643800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr12:66629800-66631800	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr12:66629800-66632000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr12:66629800-66634800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:66629800-66637400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:66629800-66644000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr12:66630000-66631200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:66630000-66631800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:66630000-66631800	Enhancers	GM12878-XiMat	blood
29	chr12:66630000-66632000	Weak transcription	Fetal Muscle Leg	muscle
30	chr12:66630000-66633200	Weak transcription	Adipose Nuclei	Adipose
31	chr12:66630000-66635000	Enhancers	Primary B cells from cord blood	blood
32	chr12:66630000-66635000	Weak transcription	NHLF	lung
33	chr12:66630000-66635400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:66630000-66637400	Weak transcription	Brain Substantia Nigra	brain
35	chr12:66630200-66632000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:66630200-66632000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:66630200-66632800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr12:66630200-66633200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:66630200-66634200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:66630200-66635200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:66630400-66631000	Enhancers	Left Ventricle	heart
42	chr12:66630400-66631000	Enhancers	Psoas Muscle	Psoas
43	chr12:66630400-66631200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr12:66630400-66632400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr12:66630400-66632800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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