Variant report

Variant	esv3397167
Chromosome Location	chr19:40174681-40175256
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	chr19:40174793-40175365	Hela-S3	cervix:	n/a	n/a
2	EP300	chr19:40174929-40175340	Hela-S3	cervix:	n/a	n/a
3	FOS	chr19:40174982-40175233	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr19:40174937-40175231	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr19:40174937-40175213	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr19:40174921-40175246	MCF10A-Er-Src	breast:	n/a	n/a
7	FOSL2	chr19:40174885-40175223	HepG2	liver:	n/a	n/a
8	JUN	chr19:40174888-40175347	Hela-S3	cervix:	n/a	n/a
9	JUN	chr19:40174968-40175168	HepG2	liver:	n/a	n/a
10	JUND	chr19:40174980-40175189	H1-hESC	embryonic stem cell:	n/a	chr19:40175084-40175095
11	JUND	chr19:40174942-40175239	HepG2	liver:	n/a	chr19:40175084-40175095
12	JUND	chr19:40174866-40175308	Hela-S3	cervix:	n/a	chr19:40175084-40175095
13	RAD21	chr19:40174954-40175310	Hela-S3	cervix:	n/a	n/a
14	RCOR1	chr19:40174885-40175339	Hela-S3	cervix:	n/a	n/a
15	RFX5	chr19:40174864-40175282	Hela-S3	cervix:	n/a	n/a
16	TCF7L2	chr19:40174921-40175297	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
ENSG00000269460	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs7259169	chr19:40174688-40174689	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs7259291	chr19:40174710-40174711	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
3	rs555688568	chr19:40174753-40174754	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs146214107	chr19:40174765-40174766	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs544814024	chr19:40174785-40174786	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs45623444	chr19:40174808-40174809	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs59155776	chr19:40174870-40174871	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs142817450	chr19:40174874-40174875	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs564823415	chr19:40174923-40174924	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs539043249	chr19:40174924-40174925	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs186650726	chr19:40174926-40174927	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs192335692	chr19:40174928-40174929	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs146945543	chr19:40174929-40174930	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs560817823	chr19:40174934-40174935	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs183424531	chr19:40174960-40174961	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs531432642	chr19:40174988-40174989	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs549550718	chr19:40175011-40175012	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs571226251	chr19:40175021-40175022	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs550548503	chr19:40175024-40175025	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs138025350	chr19:40175038-40175039	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs149494590	chr19:40175083-40175084	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs566820566	chr19:40175101-40175102	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs533928917	chr19:40175111-40175112	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs188362738	chr19:40175112-40175113	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs143871623	chr19:40175139-40175140	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs566222875	chr19:40175186-40175187	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs73557810	chr19:40175196-40175197	Enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs568765450	chr19:40175200-40175201	Enhancers Weak transcription Strong transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs578255261	chr19:40175218-40175219	Enhancers Weak transcription Strong transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs148619356	chr19:40175240-40175241	Enhancers Weak transcription Strong transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs376349104	chr19:40175244-40175245	Enhancers Weak transcription Strong transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs559901371	chr19:40175251-40175252	Enhancers Weak transcription Strong transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:65)

Disease	PMID	Source
Myelodysplastic syndrome	17634407	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Cancer	21637783	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Ovarian cancer	21720365	CNVD
Cancer	20164919	CNVD
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Autism	22495311	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Ductal carcinoma	22052326	CNVD
Pleomorphic liposarcoma	18784837	CNVD
Congenital nephrotic syndrome	18421352	CNVD
Astrocytoma	17934521	CNVD
Leukemia	17361228	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Breast cancer	21858162	CNVD
Breast cancer	17603634	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Endometrial cancer	22040021	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Oligodendroglial tumors	17285580	CNVD
renal disease	20603712	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Disorders of sex development	21048976	CNVD
Ovarian cancer	22174824	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	21364760	CNVD
Invasive pancreatic ductal carcinoma	18765526	CNVD
Rhabdomyosarcoma	16790082	CNVD
Chordoma	18071362	CNVD
Urothelial carcinoma	21177765	CNVD
small cell lung cancer	20016488	CNVD
Wilms tumour	21544195	CNVD
Mental retardation	19951919	CNVD
19q13.11 deletion syndrome	22378287	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21045282	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Ovarian neoplasms	16753589	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	CNVD
Lung cancer	21569311	CNVD
Bladder cancer	21909424	CNVD
Medulloblastoma	16783165	CNVD
Gastric cancer	18160780	CNVD
Hepatocellular carcinoma	16750200	CNVD
Basal cell lymphoma	19029149	CNVD
Breast cancer	20409316	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Multiple myeloma	16616336	CNVD
Renal cell carcinoma	18765545	CNVD
Acute myeloid leukemia	20729466	CNVD
Lung cancer	18438408	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40170000-40184600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:40171200-40189000	Weak transcription	Psoas Muscle	Psoas
3	chr19:40171800-40177600	Weak transcription	Fetal Muscle Leg	muscle
4	chr19:40172400-40180400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr19:40173200-40175800	Strong transcription	GM12878-XiMat	blood
6	chr19:40174400-40177200	Enhancers	Placenta	Placenta
7	chr19:40174800-40175200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr19:40174800-40175800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr19:40175200-40175400	Bivalent Enhancer	HepG2	liver
10	chr19:40175200-40175600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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