Variant report

Variant	rs35971570
Chromosome Location	chr12:66564165-66564166
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	YY1	chr12:66562773-66564167	SK-N-SH	brain:	n/a	chr12:66563540-66563548 chr12:66563356-66563370
2	HA-E2F1	chr12:66562968-66564353	MCF-7	breast:	n/a	chr12:66563357-66563367 chr12:66563410-66563421
3	EP300	chr12:66562732-66564171	ECC-1	luminal epithelium:	n/a	chr12:66563358-66563367 chr12:66563912-66563926 chr12:66563563-66563570
4	E2F6	chr12:66563084-66564333	K562	blood:	n/a	chr12:66563357-66563367
5	POLR2A	chr12:66562796-66564284	HepG2	liver:	n/a	n/a
6	SIN3AK20	chr12:66562842-66564170	MCF-7	breast:	n/a	n/a
7	TBP	chr12:66562210-66564318	K562	blood:	n/a	n/a
8	CTBP2	chr12:66563170-66564312	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr12:66562710-66564173	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:66563240..66564759-chr12:66582105..66583643,2	MCF-7	breast:
2	chr12:66523792..66527078-chr12:66561013..66565049,6	MCF-7	breast:
3	chr12:66562782..66564453-chr5:148959450..148961318,2	MCF-7	breast:
4	chr12:66530596..66534894-chr12:66562580..66565717,4	K562	blood:
5	chr12:66563056..66564656-chr12:66694946..66697705,2	MCF-7	breast:
6	chr12:66523081..66526604-chr12:66560988..66564576,8	MCF-7	breast:
7	chr12:66521057..66526734-chr12:66560807..66565257,7	K562	blood:
8	chr12:66562960..66564544-chr12:66668918..66671534,2	MCF-7	breast:
9	chr10:88125321..88128301-chr12:66562414..66564569,2	K562	blood:
10	chr12:66523453..66525027-chr12:66562451..66564555,2	K562	blood:

Variant related genes	Relation type
ENSG00000228144	TF binding region
TMBIM4	TF binding region
ENSG00000182771	Chromatin interaction
ENSG00000183111	Chromatin interaction
ENSG00000256777	Chromatin interaction
ENSG00000139233	Chromatin interaction
ENSG00000155957	Chromatin interaction
ENSG00000127311	Chromatin interaction
ENSG00000239335	Chromatin interaction
ENSG00000090376	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10459263	0.93[EUR][1000 genomes]
rs10506475	0.93[EUR][1000 genomes]
rs10506479	0.93[EUR][1000 genomes]
rs10878379	0.93[EUR][1000 genomes]
rs10878380	0.93[EUR][1000 genomes]
rs10878384	0.93[EUR][1000 genomes]
rs10878387	0.93[EUR][1000 genomes]
rs10878388	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	0.93[EUR][1000 genomes]
rs11176048	0.93[EUR][1000 genomes]
rs11176050	0.93[EUR][1000 genomes]
rs11176051	0.93[EUR][1000 genomes]
rs11176058	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	0.93[EUR][1000 genomes]
rs12306484	0.90[ASN][1000 genomes]
rs12426813	0.83[EUR][1000 genomes]
rs12578364	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12578752	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12578754	0.83[EUR][1000 genomes]
rs12578801	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12578994	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12581033	0.93[EUR][1000 genomes]
rs12581836	0.93[EUR][1000 genomes]
rs12582384	0.93[EUR][1000 genomes]
rs12814331	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12814606	0.88[AFR][1000 genomes];0.86[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	0.92[EUR][1000 genomes]
rs12823414	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	0.93[EUR][1000 genomes]
rs1625441	0.82[ASN][1000 genomes]
rs17245364	0.92[AFR][1000 genomes];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	0.93[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	0.93[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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35447479	0.93[EUR][1000 genomes]
rs36073795	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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35971570	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66561600-66564400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:66562000-66564200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:66562000-66564400	Active TSS	Stomach Smooth Muscle	stomach
4	chr12:66562000-66564400	Active TSS	GM12878-XiMat	blood
5	chr12:66562000-66564400	Active TSS	HSMMtube	muscle
6	chr12:66562200-66564200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:66562200-66564400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:66562200-66564400	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr12:66562200-66564400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:66562200-66564400	Active TSS	NHLF	lung
11	chr12:66562200-66564800	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr12:66562400-66564200	Active TSS	Right Ventricle	heart
13	chr12:66562400-66564400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:66562400-66564400	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr12:66562400-66564400	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr12:66562400-66564400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:66562400-66564400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:66562400-66564400	Active TSS	Brain Germinal Matrix	brain
19	chr12:66562400-66564400	Active TSS	Colonic Mucosa	Colon
20	chr12:66562400-66564400	Active TSS	HSMM	muscle
21	chr12:66562400-66564400	Active TSS	K562	blood
22	chr12:66562400-66564600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr12:66562600-66564200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:66562600-66564200	Active TSS	Primary monocytes fromperipheralblood	blood
25	chr12:66562600-66564200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
26	chr12:66562600-66564200	Active TSS	Pancreas	Pancrea
27	chr12:66562600-66564200	Active TSS	Sigmoid Colon	Sigmoid Colon
28	chr12:66562600-66564200	Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr12:66562600-66564200	Active TSS	Stomach Mucosa	stomach
30	chr12:66562600-66564200	Active TSS	HMEC	breast
31	chr12:66562600-66564400	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr12:66562600-66564400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:66562600-66564400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:66562600-66564400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:66562600-66564400	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr12:66562600-66564400	Active TSS	Muscle Satellite Cultured Cells	--
37	chr12:66562600-66564400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:66562600-66564400	Active TSS	Aorta	Aorta
39	chr12:66562600-66564400	Active TSS	Brain Angular Gyrus	brain
40	chr12:66562600-66564400	Active TSS	Brain Anterior Caudate	brain
41	chr12:66562600-66564400	Active TSS	Brain Hippocampus Middle	brain
42	chr12:66562600-66564400	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr12:66562600-66564400	Active TSS	Brain Substantia Nigra	brain
44	chr12:66562600-66564400	Active TSS	Colon Smooth Muscle	Colon
45	chr12:66562600-66564400	Active TSS	Duodenum Mucosa	Duodenum
46	chr12:66562600-66564400	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr12:66562600-66564400	Active TSS	Fetal Intestine Small	intestine
48	chr12:66562600-66564400	Active TSS	Fetal Kidney	kidney
49	chr12:66562600-66564400	Active TSS	Fetal Muscle Leg	muscle
50	chr12:66562600-66564400	Active TSS	Fetal Stomach	stomach

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