Variant report

Variant	esv3413620
Chromosome Location	chr12:29942685-29948183
allele	n/a
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	CEBPB	chr12:29947870-29948201	Hela-S3	cervix:	n/a	chr12:29948047-29948060
2	CEBPB	chr12:29945508-29946070	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr12:29944474-29944517	GM19239	blood:	n/a	n/a
4	CTCF	chr12:29947052-29947083	GM19239	blood:	n/a	n/a
5	CTCF	chr12:29944554-29944559	GM19239	blood:	n/a	n/a
6	CTCF	chr12:29944563-29944672	GM19239	blood:	n/a	n/a
7	CTCF	chr12:29944518-29944547	GM19239	blood:	n/a	n/a
8	CTCF	chr12:29942600-29942750	GM06990	blood:	n/a	n/a
9	EP300	chr12:29947737-29948216	T-47D	breast:	n/a	n/a
10	ESR1	chr12:29947832-29948098	T-47D	breast:	n/a	n/a
11	GATA1	chr12:29946311-29946619	PBDEFetal	blood:	n/a	n/a
12	GATA3	chr12:29947758-29948123	T-47D	breast:	n/a	n/a
13	GATA3	chr12:29947920-29948213	MCF-7	breast:	n/a	n/a
14	JUN	chr12:29945480-29946774	H1-hESC	embryonic stem cell:	n/a	n/a
15	JUN	chr12:29944719-29944755	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAX	chr12:29943932-29947181	NB4	blood:	n/a	chr12:29945284-29945300 chr12:29946605-29946621 chr12:29946005-29946015 chr12:29946352-29946368 chr12:29946710-29946726 chr12:29947076-29947084 chr12:29946068-29946084 chr12:29945058-29945065 chr12:29945252-29945268 chr12:29946341-29946357 chr12:29945867-29945883 chr12:29945049-29945065 chr12:29945191-29945200 chr12:29945980-29945990
17	MAX	chr12:29943885-29947145	H1-hESC	embryonic stem cell:	n/a	chr12:29945284-29945300 chr12:29946605-29946621 chr12:29946005-29946015 chr12:29946352-29946368 chr12:29946710-29946726 chr12:29947076-29947084 chr12:29946068-29946084 chr12:29945058-29945065 chr12:29945252-29945268 chr12:29946341-29946357 chr12:29945867-29945883 chr12:29945049-29945065 chr12:29945191-29945200 chr12:29945980-29945990
18	MAX	chr12:29945760-29946146	HepG2	liver:	n/a	chr12:29946005-29946015 chr12:29946068-29946084 chr12:29945867-29945883 chr12:29945980-29945990
19	MAX	chr12:29943961-29947226	HUVEC	blood vessel:	n/a	chr12:29945284-29945300 chr12:29946605-29946621 chr12:29946005-29946015 chr12:29946352-29946368 chr12:29946710-29946726 chr12:29947076-29947084 chr12:29946068-29946084 chr12:29945058-29945065 chr12:29945252-29945268 chr12:29946341-29946357 chr12:29945867-29945883 chr12:29945049-29945065 chr12:29945191-29945200 chr12:29945980-29945990
20	MYC	chr12:29944733-29944819	H1-hESC	embryonic stem cell:	n/a	n/a
21	MYC	chr12:29947908-29948161	MCF10A-Er-Src	breast:	n/a	n/a
22	NR2C2	chr12:29943953-29947172	GM12878	blood:	n/a	n/a
23	POLR2A	chr12:29945461-29945469	A549	lung:	n/a	n/a
24	POLR2A	chr12:29946565-29946752	MCF10A-Er-Src	breast:	n/a	n/a
25	STAT3	chr12:29944001-29944004	GM12878	blood:	n/a	n/a
26	SUZ12	chr12:29943823-29947184	H1-hESC	embryonic stem cell:	n/a	n/a
27	USF2	chr12:29946832-29947010	HepG2	liver:	n/a	n/a
28	USF2	chr12:29945035-29945345	HepG2	liver:	n/a	n/a
29	ZNF143	chr12:29945478-29945666	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
TMTC1	TF binding region

Extended variants
information (count: 397 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:397 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs74082539	chr12:29942702-29942703	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs567250596	chr12:29942730-29942731	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs77859944	chr12:29942741-29942742	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs548447678	chr12:29942749-29942750	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs57212421	chr12:29942844-29942845	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs530895833	chr12:29942917-29942918	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs552293853	chr12:29943075-29943076	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs375904924	chr12:29943104-29943105	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs167318	chr12:29943124-29943125	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs546792801	chr12:29943153-29943154	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs568233093	chr12:29943183-29943184	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs117138743	chr12:29943184-29943185	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs540239865	chr12:29943190-29943191	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs140465305	chr12:29943225-29943226	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs575612233	chr12:29943231-29943232	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs539416409	chr12:29943241-29943242	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs557509320	chr12:29943242-29943243	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs115092496	chr12:29943243-29943244	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs142980894	chr12:29943244-29943245	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs368386773	chr12:29943384-29943385	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs183284528	chr12:29943396-29943397	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs574660419	chr12:29943398-29943399	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs151114549	chr12:29943438-29943439	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs187322424	chr12:29943467-29943468	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs531148946	chr12:29943477-29943478	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs546161325	chr12:29943534-29943535	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs141057722	chr12:29943541-29943542	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs150240724	chr12:29943558-29943559	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs528879192	chr12:29943628-29943629	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs547081157	chr12:29943649-29943650	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs544322131	chr12:29943653-29943654	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs568577209	chr12:29943668-29943669	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs192223027	chr12:29943697-29943698	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs80280108	chr12:29943713-29943714	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs141248634	chr12:29943714-29943715	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs539386626	chr12:29943715-29943716	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs146944763	chr12:29943744-29943745	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs566316722	chr12:29943770-29943771	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs137917441	chr12:29943772-29943773	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs532983521	chr12:29943844-29943845	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
41	rs555007141	chr12:29943871-29943872	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
42	rs149454805	chr12:29943895-29943896	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs11050431	chr12:29943923-29943924	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
44	rs574106735	chr12:29943930-29943931	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs144193863	chr12:29943951-29943952	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs575870073	chr12:29943956-29943957	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
47	rs546148728	chr12:29943959-29943960	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
48	rs148267542	chr12:29943966-29943967	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
49	rs528435101	chr12:29943972-29943973	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
50	rs116475803	chr12:29943977-29943978	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:58)

Disease	PMID	Source
Melanoma	18172304	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Myxofibrosarcoma	16751306	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Wilms tumour	21544195	CNVD
Squamous cell cancer	21044232	CNVD
Acute myeloid leukemia	16864856	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Testicular cancer	18059402	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Seminomas	18059402	CNVD
Esophageal cancer	21851588	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Testicular germ cell tumor	18059402	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	21858162	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Myelodysplastic syndrome	21251322	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Acute myeloid leukemia	21251322	CNVD
small cell lung cancer	20016488	CNVD
Neurodevelopmental disorder	22521361	CNVD
Breast cancer	21509527	CNVD
Autism	22102821	CNVD
Follicular lymphoma	18703704	CNVD
Lung cancer	18438408	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Breast cancer	17133270	CNVD
Cancer	21129771	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17899364	CNVD
Myelofibrosis	22110671	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29937200-29945400	Weak transcription	Spleen	Spleen
2	chr12:29937600-29944000	Weak transcription	Gastric	stomach
3	chr12:29937800-29943800	Weak transcription	Fetal Kidney	kidney
4	chr12:29937800-29944000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:29937800-29944200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:29941200-29943800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr12:29941400-29944000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:29942800-29944000	Weak transcription	Fetal Lung	lung
9	chr12:29943600-29943800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:29943600-29944000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:29943600-29944000	Weak transcription	Pancreas	Pancrea
12	chr12:29943800-29946800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
13	chr12:29943800-29947200	ZNF genes & repeats	Fetal Kidney	kidney
14	chr12:29944000-29944400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:29944000-29944800	ZNF genes & repeats	Fetal Brain Male	brain
16	chr12:29944000-29945600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:29944000-29946000	ZNF genes & repeats	Gastric	stomach
18	chr12:29944000-29946800	Enhancers	Pancreas	Pancrea
19	chr12:29944000-29947000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
20	chr12:29944000-29947000	ZNF genes & repeats	Dnd41	blood
21	chr12:29944000-29947200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:29944000-29947200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:29944000-29947200	ZNF genes & repeats	Fetal Lung	lung
24	chr12:29944000-29947200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
25	chr12:29944200-29944400	Enhancers	Ovary	ovary
26	chr12:29944200-29947200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
27	chr12:29944400-29945200	Weak transcription	Ovary	ovary
28	chr12:29944400-29946600	ZNF genes & repeats	Esophagus	oesophagus
29	chr12:29944600-29944800	ZNF genes & repeats	NHLF	lung
30	chr12:29944800-29947000	ZNF genes & repeats	A549	lung
31	chr12:29945000-29947000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
32	chr12:29945200-29945400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:29945200-29945400	Enhancers	Ovary	ovary
34	chr12:29945400-29946000	ZNF genes & repeats	Spleen	Spleen
35	chr12:29945400-29947000	ZNF genes & repeats	GM12878-XiMat	blood
36	chr12:29945600-29947000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:29946000-29947000	Weak transcription	Spleen	Spleen
38	chr12:29946400-29947000	Enhancers	Colon Smooth Muscle	Colon
39	chr12:29946400-29953200	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr12:29946600-29946800	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr12:29946600-29947000	Weak transcription	Esophagus	oesophagus
42	chr12:29946600-29947000	ZNF genes & repeats	Fetal Heart	heart
43	chr12:29946600-29947200	Active TSS	Fetal Brain Male	brain
44	chr12:29946800-29947000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr12:29946800-29947800	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr12:29947000-29947200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:29947000-29947200	Enhancers	Esophagus	oesophagus
48	chr12:29947000-29947200	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr12:29947000-29947200	ZNF genes & repeats	Spleen	Spleen
50	chr12:29947000-29947200	Enhancers	NHDF-Ad	bronchial

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