Variant report

Variant	esv3450161
Chromosome Location	chr6:12019874-12020378
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	chr6:12017880..12021749-chr6:12024798..12028599,4	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 98 )

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs6941620	chr6:12019902-12019903	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs560016189	chr6:12019907-12019908	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs143250976	chr6:12019926-12019927	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs542200451	chr6:12019930-12019931	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs562403527	chr6:12019940-12019941	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs189244901	chr6:12019958-12019959	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs138810224	chr6:12019984-12019985	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
8	rs569278816	chr6:12020002-12020003	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs532101978	chr6:12020016-12020017	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
10	rs551837422	chr6:12020027-12020028	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
11	rs116666775	chr6:12020034-12020035	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
12	rs114510929	chr6:12020083-12020084	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
13	rs554418724	chr6:12020126-12020127	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
14	rs568351590	chr6:12020147-12020148	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
15	rs55964029	chr6:12020191-12020192	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs140631226	chr6:12020193-12020194	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
17	rs6925772	chr6:12020241-12020242	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
18	rs16872190	chr6:12020289-12020290	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs570237602	chr6:12020300-12020301	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
20	rs181787388	chr6:12020314-12020315	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:98)

Disease	PMID	Source
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Prostate cancer	16573809	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	17603634	CNVD
Cancer	20164920	CNVD
Colorectal cancer	21297112	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Follicular lymphoma	20505157	CNVD
Glioblastoma multiforme	21080181	CNVD
Ewing''s sarcoma	21437220	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Leukemia	21518781	CNVD
Cancer	21637783	CNVD
Facial dysmorphism	22105932	CNVD
Medulloblastoma	21979893	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Hepatocellular carcinoma	22174799	CNVD
Endometrial cancer	22040021	CNVD
Acute myeloid leukemia	16864856	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Bladder cancer	19088036	CNVD
Wilms tumour	21544195	CNVD
Uveal melanoma	21693616	CNVD
Biliary cancer	19435499	CNVD
Malaria	21533027	CNVD
Retinoblastoma	19183342	CNVD
Acute myeloid leukemia	20729466	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Prostate cancer	18632612	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	21858162	CNVD
Lung cancer	18438408	CNVD
Multiple myeloma	17550852	CNVD
Ewing''s sarcoma	17952124	CNVD
Gastric cancer	16891809	CNVD
Ovarian cancer	21781307	CNVD
Autism	22495311	CNVD
Autism	21448237	CNVD
Cancer	20164919	CNVD
Melanoma	18172304	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Breast cancer	22844521	CNVD
HIV/AIDS	22844521	CNVD
Ovarian cancer	22844521	CNVD
Prostate cancer	22844521	CNVD
Psoriasis	22844521	CNVD
Rheumatoid arthritis	22844521	CNVD
Sclerosis systemic	22844521	CNVD
Systemic lupus erythematosus	22844521	CNVD
Breast cancer	22522925	CNVD
Breast cancer	21552322	CNVD
Immune disease	21076436	CNVD
Autoimmune disease	19135723	CNVD
Systemic lupus erythematosus	17953491	CNVD
Recurrent Infections	22737222	CNVD
Systemic lupus erythematosus	21904924	CNVD
Ependymoma	19289631	CNVD
small cell lung cancer	20016488	CNVD
Gestational infection	22844521	CNVD
Head circumference	22844521	CNVD
Infertility	22844521	CNVD
Recurrent birth weight diabetes	22844521	CNVD
Obesity	22844521	CNVD
Recurrent pregnancy loss	22844521	CNVD
Intellectual disability	21811512	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Congenital anomalies of the kidney and urinary tract	18694510	CNVD
Nasopharyngeal cancer	22815911	CNVD
Osteosarcoma	16790693	CNVD
Hepatocellular carcinoma	16750200	CNVD
Basal cell lymphoma	21115979	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Ovarian cancer	21720365	CNVD
Cancer	21183584	CNVD
Acute myeloid leukemia	18000384	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Breast cancer	17133270	CNVD
Breast cancer	21364760	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Bladder cancer	21909424	CNVD
Myelofibrosis	22110671	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Burkitt''s lymphoma	19759907	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Metastatic melanoma	18483359	CNVD

Chromatin state (count:137 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12013800-12033600	Weak transcription	Psoas Muscle	Psoas
2	chr6:12014000-12020400	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:12014000-12023200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:12014000-12023200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:12014000-12031800	Weak transcription	Brain Substantia Nigra	brain
6	chr6:12014400-12020200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:12014400-12023200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:12014400-12024800	Weak transcription	Stomach Mucosa	stomach
9	chr6:12014400-12030000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:12014600-12020400	Weak transcription	Fetal Heart	heart
11	chr6:12014600-12020600	Weak transcription	Right Atrium	heart
12	chr6:12014600-12021800	ZNF genes & repeats	GM12878-XiMat	blood
13	chr6:12014600-12032000	Weak transcription	Brain Angular Gyrus	brain
14	chr6:12015000-12021000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:12015000-12022000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr6:12015000-12022000	Strong transcription	Fetal Muscle Trunk	muscle
17	chr6:12015000-12022000	Strong transcription	Fetal Muscle Leg	muscle
18	chr6:12015200-12020200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:12015200-12021200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:12015200-12021400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:12015200-12021800	Strong transcription	Primary B cells from peripheral blood	blood
22	chr6:12015200-12023400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:12015200-12024600	Weak transcription	NHDF-Ad	bronchial
24	chr6:12015400-12020400	Weak transcription	Aorta	Aorta
25	chr6:12015400-12021000	Strong transcription	NHLF	lung
26	chr6:12015400-12021400	Strong transcription	NHEK	skin
27	chr6:12015400-12023200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:12015400-12025000	Weak transcription	Small Intestine	intestine
29	chr6:12015400-12025400	Strong transcription	Liver	Liver
30	chr6:12015400-12029200	Weak transcription	Brain Anterior Caudate	brain
31	chr6:12015400-12034000	Weak transcription	Hela-S3	cervix
32	chr6:12015600-12022000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:12015600-12023000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr6:12016000-12021800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr6:12016000-12022000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:12016200-12020800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr6:12016200-12022000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:12016400-12020800	Strong transcription	Fetal Lung	lung
39	chr6:12016400-12022000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:12016800-12022000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:12017000-12020600	Strong transcription	Spleen	Spleen
42	chr6:12017000-12021000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:12017000-12021000	Strong transcription	Rectal Smooth Muscle	rectum
44	chr6:12017000-12021000	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr6:12017000-12022400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr6:12017000-12023400	Strong transcription	Fetal Intestine Small	intestine
47	chr6:12017200-12020600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:12017200-12021800	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr6:12017600-12020800	Strong transcription	Lung	lung
50	chr6:12017600-12022000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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