Variant report

Variant	rs561783408
Chromosome Location	chr12:29937199-29937200
allele	A/G
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	chr12:29936504-29937566	HEK293	kidney:	n/a	n/a
2	REST	chr12:29937067-29937490	SK-N-SH	brain:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937287-29937307 chr12:29937442-29937450 chr12:29937287-29937307 chr12:29937287-29937307
3	POLR2A	chr12:29937161-29937582	H1-hESC	embryonic stem cell:	n/a	n/a
4	REST	chr12:29936950-29937571	PANC-1	pancreas:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937058-29937068 chr12:29937287-29937307 chr12:29937442-29937450 chr12:29937287-29937307 chr12:29937287-29937307
5	SMC3	chr12:29936835-29937613	Hela-S3	cervix:	n/a	chr12:29936835-29936845
6	REST	chr12:29936965-29937541	U87	brain:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937058-29937068 chr12:29937287-29937307 chr12:29937442-29937450 chr12:29937287-29937307 chr12:29937287-29937307
7	REST	chr12:29937130-29937454	PANC-1	pancreas:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937287-29937307 chr12:29937442-29937450 chr12:29937287-29937307 chr12:29937287-29937307
8	REST	chr12:29936872-29937625	HL-60	blood:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937058-29937068 chr12:29937287-29937307 chr12:29937442-29937450 chr12:29937287-29937307 chr12:29937287-29937307
9	REST	chr12:29936501-29937644	ECC-1	luminal epithelium:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937058-29937068 chr12:29936820-29936833 chr12:29937287-29937307 chr12:29937442-29937450 chr12:29937287-29937307 chr12:29937287-29937307
10	SIN3A	chr12:29934958-29937743	H1-hESC	embryonic stem cell:	n/a	chr12:29936999-29937010 chr12:29936827-29936838 chr12:29937288-29937302 chr12:29937289-29937298 chr12:29937059-29937068 chr12:29935826-29935837
11	ZNF263	chr12:29935067-29937647	HEK293-T-REx	kidney:	n/a	n/a
12	CHD2	chr12:29936639-29937431	Hela-S3	cervix:	n/a	chr12:29936887-29936897
13	MAZ	chr12:29935094-29937598	Hela-S3	cervix:	n/a	chr12:29936882-29936892 chr12:29937117-29937126
14	ZBTB7A	chr12:29936501-29937551	ECC-1	luminal epithelium:	n/a	n/a
15	SIN3AK20	chr12:29937123-29937442	H1-hESC	embryonic stem cell:	n/a	n/a
16	REST	chr12:29936665-29937515	U87	brain:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937058-29937068 chr12:29936820-29936833 chr12:29937287-29937307 chr12:29937442-29937450 chr12:29937287-29937307 chr12:29937287-29937307
17	REST	chr12:29937127-29937498	H1-hESC	embryonic stem cell:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937287-29937307 chr12:29937442-29937450 chr12:29937287-29937307 chr12:29937287-29937307
18	REST	chr12:29936901-29937541	U87	brain:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937058-29937068 chr12:29937287-29937307 chr12:29937442-29937450 chr12:29937287-29937307 chr12:29937287-29937307
19	REST	chr12:29937121-29937460	U87	brain:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937287-29937307 chr12:29937442-29937450 chr12:29937287-29937307 chr12:29937287-29937307
20	REST	chr12:29937179-29937415	HepG2	liver:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937287-29937307 chr12:29937287-29937307 chr12:29937287-29937307
21	MAX	chr12:29935040-29937585	Hela-S3	cervix:	n/a	chr12:29936882-29936892 chr12:29937117-29937126
22	POLR2A	chr12:29935133-29937633	Hela-S3	cervix:	n/a	n/a
23	MAZ	chr12:29934937-29937647	IMR90	lung:	n/a	chr12:29936882-29936892 chr12:29937117-29937126
24	REST	chr12:29937027-29937589	MCF-7	breast:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937058-29937068 chr12:29937287-29937307 chr12:29937442-29937450 chr12:29937287-29937307 chr12:29937287-29937307
25	REST	chr12:29937063-29937521	PFSK-1	brain:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937287-29937307 chr12:29937442-29937450 chr12:29937287-29937307 chr12:29937287-29937307
26	REST	chr12:29936948-29937614	PANC-1	pancreas:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937058-29937068 chr12:29937287-29937307 chr12:29937442-29937450 chr12:29937287-29937307 chr12:29937287-29937307
27	TAF1	chr12:29936644-29937376	ECC-1	luminal epithelium:	n/a	n/a
28	E2F4	chr12:29937151-29937455	MCF10A-Er-Src	breast:	n/a	n/a
29	BACH1	chr12:29937171-29937398	H1-hESC	embryonic stem cell:	n/a	n/a
30	REST	chr12:29937165-29937437	PANC-1	pancreas:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937287-29937307 chr12:29937287-29937307 chr12:29937287-29937307
31	REST	chr12:29937090-29937402	PFSK-1	brain:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937287-29937307 chr12:29937287-29937307 chr12:29937287-29937307
32	REST	chr12:29937021-29937520	Hela-S3	cervix:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937058-29937068 chr12:29937287-29937307 chr12:29937442-29937450 chr12:29937287-29937307 chr12:29937287-29937307
33	TEAD4	chr12:29937116-29937598	A549	lung:	n/a	n/a
34	ZBTB7A	chr12:29936524-29937547	ECC-1	luminal epithelium:	n/a	n/a
35	REST	chr12:29937122-29937446	A549	lung:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937287-29937307 chr12:29937287-29937307 chr12:29937287-29937307
36	REST	chr12:29937121-29937410	HepG2	liver:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937287-29937307 chr12:29937287-29937307 chr12:29937287-29937307
37	ZNF143	chr12:29937159-29937388	H1-hESC	embryonic stem cell:	n/a	chr12:29937309-29937319
38	REST	chr12:29936867-29937536	SK-N-SH	brain:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937058-29937068 chr12:29937287-29937307 chr12:29937442-29937450 chr12:29937287-29937307 chr12:29937287-29937307
39	REST	chr12:29936922-29937471	Hela-S3	cervix:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937058-29937068 chr12:29937287-29937307 chr12:29937442-29937450 chr12:29937287-29937307 chr12:29937287-29937307
40	CHD1	chr12:29934973-29937715	IMR90	lung:	n/a	chr12:29936887-29936897
41	REST	chr12:29937082-29937467	MCF-7	breast:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937287-29937307 chr12:29937442-29937450 chr12:29937287-29937307 chr12:29937287-29937307
42	MXI1	chr12:29934395-29937646	IMR90	lung:	n/a	n/a
43	REST	chr12:29936920-29937564	A549	lung:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937058-29937068 chr12:29937287-29937307 chr12:29937442-29937450 chr12:29937287-29937307 chr12:29937287-29937307
44	REST	chr12:29937148-29937511	H1-hESC	embryonic stem cell:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937287-29937307 chr12:29937442-29937450 chr12:29937287-29937307 chr12:29937287-29937307
45	SMARCB1	chr12:29935592-29937600	Hela-S3	cervix:	n/a	n/a
46	MAZ	chr12:29937140-29937215	GM12878	blood:	n/a	n/a
47	REST	chr12:29937075-29937443	GM12878	blood:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937287-29937307 chr12:29937287-29937307 chr12:29937287-29937307
48	RCOR1	chr12:29934833-29937689	IMR90	lung:	n/a	n/a
49	REST	chr12:29936879-29937454	HepG2	liver:	n/a	chr12:29937289-29937299 chr12:29937287-29937301 chr12:29937058-29937068 chr12:29937287-29937307 chr12:29937442-29937450 chr12:29937287-29937307 chr12:29937287-29937307
50	TCF12	chr12:29936713-29937547	ECC-1	luminal epithelium:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:29937188-29937238	HAEpiC	amniotic membrane:	n/a
2	chr12:29937188-29937238	HCT-116	colon:	n/a
3	chr12:29937188-29937238	NHBE	bronchial:	n/a
4	chr12:29937188-29937238	AG09309	skin:	n/a
5	chr12:29937188-29937238	SK-N-SH	brain:	n/a
6	chr12:29937188-29937238	HepG2	liver:	n/a
7	chr12:29937188-29937238	NB4	blood:	n/a
8	chr12:29937188-29937238	AG04450	lung:	fetal
9	chr12:29937188-29937238	Hela-S3	cervix:	n/a
10	chr12:29937188-29937238	BJ	skin:	n/a
11	chr12:29937188-29937238	HCM	heart:	n/a
12	chr12:29937188-29937238	AG09319	gingival:	n/a
13	chr12:29937188-29937238	NH-A	brain:	n/a
14	chr12:29937188-29937238	AoSMC	blood vessel:	n/a
15	chr12:29937188-29937238	HL-60	blood:	n/a
16	chr12:29937188-29937238	IMR90	lung:	fetal
17	chr12:29937188-29937238	PFSK-1	brain:	n/a
18	chr12:29937188-29937238	HRCEpiC	kidney:	n/a
19	chr12:29937188-29937238	RPTEC	kidney:	n/a
20	chr12:29937188-29937238	AG10803	skin:	n/a
21	chr12:29937188-29937238	GM19239	blood:	n/a
22	chr12:29937188-29937238	GM12891	blood:	n/a
23	chr12:29937188-29937238	HRPEpiC	eye:	n/a
24	chr12:29937188-29937238	NT2-D1	testis:	n/a
25	chr12:29937188-29937238	ProgFib	skin:	n/a
26	chr12:29937188-29937238	LNCaP	prostate:	n/a
27	chr12:29937188-29937238	Hepatocyte	liver:	n/a
28	chr12:29937188-29937238	MCF-7	breast:	n/a
29	chr12:29937188-29937238	HNPCEpiC	eye:	n/a
30	chr12:29937188-29937238	AG04449	skin:	fetal
31	chr12:29937188-29937238	Caco-2	colon:	n/a
32	chr12:29937188-29937238	GM12878	blood:	n/a
33	chr12:29937188-29937238	K562	blood:	n/a
34	chr12:29937188-29937238	HPAEpiC	pulmonary alveolar:	n/a
35	chr12:29937188-29937238	PrEC	prostate:	n/a
36	chr12:29937188-29937238	HIPEpiC	eye:	n/a
37	chr12:29937188-29937238	HCF	heart:	n/a
38	chr12:29937188-29937238	SK-N-MC	brain:	n/a
39	chr12:29937188-29937238	HMEC	breast:	n/a
40	chr12:29937188-29937238	H1-hESC	embryonic stem cell:	embryo
41	chr12:29937188-29937238	HCPEpiC	choroid plexus:	n/a
42	chr12:29937188-29937238	PANC-1	pancreas:	n/a
43	chr12:29937188-29937238	GM12892	blood:	n/a
44	chr12:29937188-29937238	CMK	blood:	n/a
45	chr12:29937188-29937238	T-47D	breast:	n/a
46	chr12:29937188-29937238	NHDF-neo	bronchial:	n/a
47	chr12:29937188-29937238	A549	lung:	n/a
48	chr12:29937188-29937238	ECC-1	luminal epithelium:	n/a
49	chr12:29937188-29937238	SAEC	small airway:	n/a
50	chr12:29937188-29937238	MCF10A-Er-Src	breast:	n/a

Variant related genes	Relation type
TMTC1	TF binding region
TMTC1	CpG island

Extended variants
information (count: 4 )
Associated
traits (count: 0)

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	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv898953	chr12:29905322-29989292	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv826294	chr12:29934604-29940372	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
4	esv3400754	chr12:29935710-29938558	Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29933000-29937800	Active TSS	Aorta	Aorta
2	chr12:29933800-29937800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:29934000-29937800	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr12:29934000-29937800	Active TSS	Fetal Kidney	kidney
5	chr12:29934000-29937800	Active TSS	NHLF	lung
6	chr12:29934000-29938000	Active TSS	Right Ventricle	heart
7	chr12:29934200-29937400	Active TSS	Lung	lung
8	chr12:29934200-29937600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
9	chr12:29934200-29937600	Active TSS	Rectal Smooth Muscle	rectum
10	chr12:29934200-29937800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:29934400-29937600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:29934400-29937600	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr12:29934400-29937600	Bivalent/Poised TSS	Thymus	Thymus
14	chr12:29934400-29937800	Active TSS	Brain Anterior Caudate	brain
15	chr12:29934400-29937800	Active TSS	Brain Hippocampus Middle	brain
16	chr12:29934400-29937800	Active TSS	Fetal Brain Female	brain
17	chr12:29934600-29937400	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr12:29934600-29937800	Active TSS	Right Atrium	heart
19	chr12:29934600-29937800	Active TSS	Stomach Smooth Muscle	stomach
20	chr12:29934800-29937400	Active TSS	Rectal Mucosa Donor 31	rectum
21	chr12:29934800-29937400	Bivalent/Poised TSS	NHEK	skin
22	chr12:29934800-29937600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:29934800-29937600	Active TSS	Brain Cingulate Gyrus	brain
24	chr12:29934800-29937600	Active TSS	Brain Substantia Nigra	brain
25	chr12:29934800-29937800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:29934800-29937800	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr12:29934800-29937800	Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr12:29934800-29937800	Active TSS	Left Ventricle	heart
29	chr12:29934800-29937800	Active TSS	Ovary	ovary
30	chr12:29934800-29937800	Active TSS	Psoas Muscle	Psoas
31	chr12:29934800-29937800	Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr12:29934800-29937800	Active TSS	HSMM	muscle
33	chr12:29935000-29937200	Active TSS	Primary monocytes fromperipheralblood	blood
34	chr12:29935000-29937400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:29935000-29937400	Active TSS	HMEC	breast
36	chr12:29935000-29937800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr12:29935000-29937800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:29935000-29937800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:29935000-29937800	Active TSS	Brain Angular Gyrus	brain
40	chr12:29935000-29937800	Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr12:29935000-29937800	Active TSS	Hela-S3	cervix
42	chr12:29935000-29937800	Active TSS	HSMMtube	muscle
43	chr12:29935200-29937200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:29935200-29937200	Active TSS	Spleen	Spleen
45	chr12:29935200-29937600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr12:29935200-29937600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
47	chr12:29935200-29937800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:29935200-29937800	Active TSS	Muscle Satellite Cultured Cells	--
49	chr12:29935200-29937800	Active TSS	NHDF-Ad	bronchial
50	chr12:29935400-29937600	Active TSS	Colon Smooth Muscle	Colon

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