Variant report

Variant	esv3346863
Chromosome Location	chr16:12659225-12659457
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12656706..12658781-chr16:12659071..12661791,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 68 )

Variant overlapped rSNPs/rCNVs (count:42 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs55910004	chr16:12659229-12659230	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs541320216	chr16:12659231-12659232	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs145758378	chr16:12659240-12659241	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs558095112	chr16:12659241-12659242	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs574901263	chr16:12659242-12659243	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs544099750	chr16:12659245-12659246	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs560890508	chr16:12659252-12659253	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs180895188	chr16:12659262-12659263	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs377500322	chr16:12659282-12659283	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs540450702	chr16:12659286-12659287	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs9921087	chr16:12659287-12659288	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs528555139	chr16:12659289-12659290	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs34392084	chr16:12659290-12659291	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs386384286	chr16:12659291-12659292	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs397693489	chr16:12659292-12659293	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs543290591	chr16:12659302-12659303	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs559027034	chr16:12659308-12659309	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs565229452	chr16:12659312-12659313	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs563506024	chr16:12659317-12659318	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs12708750	chr16:12659325-12659326	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs12918863	chr16:12659339-12659340	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs189809448	chr16:12659353-12659354	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs138261588	chr16:12659354-12659355	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs149198486	chr16:12659358-12659359	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs566967680	chr16:12659360-12659361	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs12443688	chr16:12659361-12659362	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs9921116	chr16:12659363-12659364	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs574884678	chr16:12659365-12659366	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs537484890	chr16:12659369-12659370	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs554423110	chr16:12659370-12659371	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs76893140	chr16:12659388-12659389	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs527714141	chr16:12659390-12659391	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs11639553	chr16:12659391-12659392	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs565416289	chr16:12659393-12659394	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs12918996	chr16:12659407-12659408	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs551021293	chr16:12659422-12659423	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs72775235	chr16:12659427-12659428	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs375357749	chr16:12659430-12659431	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs12708751	chr16:12659435-12659436	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs546986338	chr16:12659440-12659441	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs567239189	chr16:12659444-12659445	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs567007094	chr16:12659455-12659456	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:68)

Disease	PMID	Source
Cancer	21183584	CNVD
Follicular lymphoma	20505157	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	17603634	CNVD
Hodgkin''s lymphoma	20651079	CNVD
Metanephric adenoma	20802469	CNVD
Melanoma	18172304	CNVD
Breast cancer	16608533	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17133270	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Lung adenocarcinoma	17086460	CNVD
Lung cancer	17086460	CNVD
Autism	22566537	CNVD
Intellectual disability	22566537	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Autism	19415332	CNVD
Medulloblastoma	21979893	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Schizophrenia	22958593	CNVD
Lung cancer	18438408	CNVD
Ductal carcinoma	22052326	CNVD
Breast cancer	21509527	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22102821	CNVD
Autism	22495311	CNVD
idiopathic generalized epilepsy	19843651	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Intellectual disability	22102821	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Hodgkin''s lymphoma	17606441	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Prostate cancer	18632612	CNVD
Schizophrenia	20587603	CNVD
Schizophrenia	20553308	CNVD
Autism	19786961	CNVD
Mental retardation	19786961	CNVD
Schizophrenia	19786961	CNVD
Mental retardation	19951919	CNVD
Autism	18791038	CNVD
Splenic marginal zone lymphoma	18492102	CNVD
Malignant germ cell tumour	17285132	CNVD
Autism	17480035	CNVD
Schizophrenia	19955444	CNVD
Breast cancer	21858162	CNVD
Myelofibrosis	22110671	CNVD
Mental retardation	17847001	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12613000-12670800	Weak transcription	Pancreas	Pancrea
2	chr16:12632800-12663800	Weak transcription	Aorta	Aorta
3	chr16:12641200-12667000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr16:12642000-12662200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr16:12645200-12661600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr16:12646000-12661000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr16:12646200-12659800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr16:12646200-12660000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr16:12646400-12659400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr16:12646400-12660800	Weak transcription	Thymus	Thymus
11	chr16:12647400-12662200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr16:12647400-12665200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr16:12647600-12661600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr16:12648000-12662200	Weak transcription	Fetal Stomach	stomach
15	chr16:12648400-12668800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr16:12649800-12662200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr16:12652200-12660200	Strong transcription	Primary B cells from cord blood	blood
18	chr16:12652200-12669200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr16:12652400-12666400	Weak transcription	Brain Anterior Caudate	brain
20	chr16:12652600-12665800	Weak transcription	Brain Angular Gyrus	brain
21	chr16:12652600-12672200	Weak transcription	Right Ventricle	heart
22	chr16:12652800-12663400	Weak transcription	Brain Substantia Nigra	brain
23	chr16:12653200-12662200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr16:12653200-12667600	Weak transcription	Brain Hippocampus Middle	brain
25	chr16:12653200-12669200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr16:12653400-12659800	Weak transcription	Ovary	ovary
27	chr16:12653600-12662400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr16:12653600-12662600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr16:12653600-12663200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr16:12653800-12662600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr16:12653800-12665800	Weak transcription	NHDF-Ad	bronchial
32	chr16:12654800-12659600	Strong transcription	Primary T cells from cord blood	blood
33	chr16:12656000-12661600	Weak transcription	Spleen	Spleen
34	chr16:12656000-12662200	Weak transcription	Gastric	stomach
35	chr16:12656400-12664200	Weak transcription	Left Ventricle	heart
36	chr16:12656800-12660200	ZNF genes & repeats	GM12878-XiMat	blood
37	chr16:12657600-12664400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr16:12658200-12659600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
39	chr16:12658600-12659800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
40	chr16:12658800-12659600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
41	chr16:12659000-12659600	ZNF genes & repeats	Lung	lung
42	chr16:12659000-12660200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
43	chr16:12659000-12661800	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr16:12659200-12659600	ZNF genes & repeats	Adipose Nuclei	Adipose
45	chr16:12659200-12659600	ZNF genes & repeats	Esophagus	oesophagus
46	chr16:12659200-12659600	ZNF genes & repeats	Placenta	Placenta
47	chr16:12659200-12662200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr16:12659400-12659600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
49	chr16:12659400-12659600	Enhancers	Fetal Thymus	thymus
50	chr16:12659400-12662000	Enhancers	Primary T cells fromperipheralblood	blood

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