Variant report

Variant	rs1152908
Chromosome Location	chr12:66629504-66629505
allele	A/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	CTCF	chr12:66629380-66629530	HAc	cerebellar:	n/a	n/a
2	CTCF	chr12:66629380-66629530	AG04450	lung:	n/a	n/a
3	CTCF	chr12:66629400-66629550	HCM	heart:	n/a	n/a
4	GATA1	chr12:66628774-66629896	PBDE	blood:	n/a	chr12:66629795-66629805 chr12:66629796-66629805 chr12:66629792-66629808 chr12:66629794-66629806
5	RFX5	chr12:66627198-66630145	SK-N-SH	brain:	n/a	chr12:66628021-66628036
6	POLR2A	chr12:66628935-66629519	HL-60	blood:	n/a	n/a
7	POLR2A	chr12:66628863-66629650	HUVEC	blood vessel:	n/a	n/a
8	CTCF	chr12:66629480-66629630	NHDF-neo	bronchial:	n/a	n/a
9	POLR2A	chr12:66628987-66629527	HL-60	blood:	n/a	n/a
10	RFX5	chr12:66629308-66629791	K562	blood:	n/a	n/a
11	POLR2A	chr12:66628855-66629507	ProgFib	skin:	n/a	n/a
12	POLR2A	chr12:66628835-66629580	MCF-7	breast:	n/a	n/a
13	CTCF	chr12:66629360-66629510	NHLF	lung:	n/a	n/a
14	POLR2A	chr12:66628909-66629553	Gliobla	brain:	n/a	n/a
15	POLR2A	chr12:66628804-66629553	H1-hESC	embryonic stem cell:	n/a	n/a

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

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1152906	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1152907	0.81[AMR][1000 genomes]
rs1152909	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168641	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168642	0.86[EUR][1000 genomes]
rs1168643	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1168644	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1168647	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1168648	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1168762	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1370127	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1370128	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1623665	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1624395	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1732877	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[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
rs1152908	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

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	chr12:66628200-66629800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr12:66628200-66629800	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr12:66628400-66630000	Active TSS	Osteobl	bone
6	chr12:66628600-66629600	Active TSS	H9 Cell Line	embryonic stem cell
7	chr12:66628600-66629600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:66628600-66629600	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr12:66628600-66629600	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr12:66628600-66629600	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr12:66628600-66629600	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr12:66628600-66629600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:66628600-66629600	Active TSS	Primary B cells from cord blood	blood
14	chr12:66628600-66629600	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr12:66628600-66629600	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr12:66628600-66629600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:66628600-66629600	Active TSS	Brain Angular Gyrus	brain
18	chr12:66628600-66629600	Active TSS	Brain Hippocampus Middle	brain
19	chr12:66628600-66629600	Active TSS	Brain Substantia Nigra	brain
20	chr12:66628600-66629600	Active TSS	Right Atrium	heart
21	chr12:66628600-66629800	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr12:66628600-66629800	Active TSS	Primary T cells from cord blood	blood
23	chr12:66628600-66629800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:66628600-66629800	Active TSS	Stomach Smooth Muscle	stomach
25	chr12:66628600-66630000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:66628600-66630000	Active TSS	Muscle Satellite Cultured Cells	--
27	chr12:66628600-66630000	Active TSS	A549	lung
28	chr12:66628600-66630000	Active TSS	HMEC	breast
29	chr12:66628600-66630200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:66628600-66630400	Active TSS	Brain Anterior Caudate	brain
31	chr12:66628800-66629600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:66628800-66629600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:66628800-66629600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:66628800-66629600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr12:66628800-66629600	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
36	chr12:66628800-66629600	Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr12:66628800-66629600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
38	chr12:66628800-66629600	Active TSS	Brain Germinal Matrix	brain
39	chr12:66628800-66629600	Active TSS	Colonic Mucosa	Colon
40	chr12:66628800-66629600	Active TSS	Duodenum Mucosa	Duodenum
41	chr12:66628800-66629600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr12:66628800-66629600	Active TSS	Fetal Brain Female	brain
43	chr12:66628800-66629600	Active TSS	Fetal Muscle Trunk	muscle
44	chr12:66628800-66629600	Active TSS	Ovary	ovary
45	chr12:66628800-66629600	Active TSS	Psoas Muscle	Psoas
46	chr12:66628800-66629600	Active TSS	Thymus	Thymus
47	chr12:66628800-66629600	Active TSS	HSMM	muscle
48	chr12:66628800-66629600	Active TSS	Monocytes-CD14+_RO01746	blood
49	chr12:66628800-66629800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:66628800-66629800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood

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