Variant report

Variant	esv3399950
Chromosome Location	chr6:1735853-1740351
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	chr6:1714828..1716630-chr6:1737875..1739669,2	MCF-7	breast:
2	chr6:1728980..1730810-chr6:1735730..1738252,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXC1-8	chr6:1740270-1740480	NONHSAT106545
2	lnc-FOXC1-8	chr6:1739435-1739570	NONHSAT106545
3	lnc-FOXC1-8	chr6:1739800-1739957	NONHSAT106545

Extended variants
information (count: 262 )
Associated
traits (count: 71 )

Variant overlapped rSNPs/rCNVs (count:262 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs73425374	chr6:1735913-1735914	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs370855625	chr6:1735932-1735933	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs532557468	chr6:1735934-1735935	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs572980654	chr6:1735935-1735936	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs538757290	chr6:1735960-1735961	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs558660850	chr6:1735989-1735990	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs575317656	chr6:1735995-1735996	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs117328380	chr6:1736003-1736004	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs574722183	chr6:1736037-1736038	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs568443058	chr6:1736055-1736056	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs540658274	chr6:1736083-1736084	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs376019109	chr6:1736087-1736088	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs560934699	chr6:1736179-1736180	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs551374026	chr6:1736201-1736202	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs144290450	chr6:1736222-1736223	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs375576530	chr6:1736230-1736231	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs560535671	chr6:1736249-1736250	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs532539229	chr6:1736275-1736276	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs78298205	chr6:1736310-1736311	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs191534463	chr6:1736334-1736335	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs562603219	chr6:1736361-1736362	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs368573866	chr6:1736438-1736439	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs548225421	chr6:1736472-1736473	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs148448266	chr6:1736489-1736490	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs536190529	chr6:1736496-1736497	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs7760724	chr6:1736501-1736502	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs184020638	chr6:1736527-1736528	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs142625711	chr6:1736529-1736530	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs551266666	chr6:1736532-1736533	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs541198301	chr6:1736560-1736561	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs558773363	chr6:1736576-1736577	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs151005983	chr6:1736577-1736578	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs188750896	chr6:1736582-1736583	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs564696939	chr6:1736588-1736589	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs530773334	chr6:1736595-1736596	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs554301963	chr6:1736605-1736606	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs139986973	chr6:1736646-1736647	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs193198526	chr6:1736654-1736655	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs185506614	chr6:1736689-1736690	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs577033692	chr6:1736748-1736749	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs34784799	chr6:1736757-1736758	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs190765582	chr6:1736773-1736774	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs3800031	chr6:1736904-1736905	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs369556784	chr6:1736920-1736921	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs371816816	chr6:1736945-1736946	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs542295971	chr6:1736997-1736998	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs556906154	chr6:1736999-1737000	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs561957198	chr6:1737007-1737008	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs80313170	chr6:1737016-1737017	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs373892493	chr6:1737037-1737038	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:71)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Myelofibrosis	22110671	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Prader-willi syndrome	20588305	CNVD
Multiple myeloma	16616336	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Developmental delay	19490664	CNVD
Cancer	21183584	CNVD
Multiple Epiphyseal Dysplasia	20877625	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Glaucoma	18694899	CNVD
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
Thoracic aortic aneurysm	21092924	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Prostate cancer	18632612	CNVD
Myelodysplastic syndrome	21251322	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Breast cancer	21858162	CNVD
Breast cancer	21364760	CNVD
Lung cancer	18438408	CNVD
Bladder cancer	21909424	CNVD
Multiple myeloma	17550852	CNVD
Ewing''s sarcoma	17952124	CNVD
Cancer	20164919	CNVD
Gastric cancer	16891809	CNVD
Ovarian cancer	21781307	CNVD
small cell lung cancer	20016488	CNVD
Autism	22495311	CNVD
Autism	21448237	CNVD
Lung adenocarcinoma	21935476	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1701200-1749400	Weak transcription	Colonic Mucosa	Colon
2	chr6:1716000-1749200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:1721200-1746200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:1721200-1748800	Weak transcription	Osteobl	bone
5	chr6:1721400-1739400	Weak transcription	Hela-S3	cervix
6	chr6:1723000-1743200	Strong transcription	HepG2	liver
7	chr6:1725000-1737800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:1726800-1749000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr6:1726800-1749000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:1727000-1737600	Weak transcription	Primary T cells from cord blood	blood
11	chr6:1731000-1736400	Weak transcription	GM12878-XiMat	blood
12	chr6:1731800-1745000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:1731800-1746200	Weak transcription	Right Atrium	heart
14	chr6:1732200-1744800	Weak transcription	Aorta	Aorta
15	chr6:1732200-1750600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:1732200-1756600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:1735400-1736000	Enhancers	Esophagus	oesophagus
18	chr6:1735400-1736000	Genic enhancers	Gastric	stomach
19	chr6:1735600-1736000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:1735600-1736000	Enhancers	Pancreas	Pancrea
21	chr6:1735600-1737000	Enhancers	Stomach Mucosa	stomach
22	chr6:1735800-1736000	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr6:1735800-1736400	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr6:1735800-1738000	Weak transcription	Spleen	Spleen
25	chr6:1735800-1741600	Weak transcription	Fetal Intestine Small	intestine
26	chr6:1736000-1737600	Weak transcription	Gastric	stomach
27	chr6:1736000-1737800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:1736000-1737800	Weak transcription	Pancreas	Pancrea
29	chr6:1736000-1746200	Weak transcription	Esophagus	oesophagus
30	chr6:1736000-1746200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr6:1736400-1739200	Enhancers	GM12878-XiMat	blood
32	chr6:1736400-1746200	Weak transcription	Right Ventricle	heart
33	chr6:1737000-1737200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:1737000-1737200	Enhancers	Primary B cells from peripheral blood	blood
35	chr6:1737000-1737200	Enhancers	Brain Germinal Matrix	brain
36	chr6:1737000-1749000	Weak transcription	Stomach Mucosa	stomach
37	chr6:1737200-1737400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:1737200-1737600	Weak transcription	Fetal Kidney	kidney
39	chr6:1737200-1738000	Weak transcription	Primary B cells from peripheral blood	blood
40	chr6:1737200-1738200	Weak transcription	Brain Germinal Matrix	brain
41	chr6:1737400-1746200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:1737600-1737800	Enhancers	Fetal Kidney	kidney
43	chr6:1737600-1738400	Strong transcription	Primary T cells from cord blood	blood
44	chr6:1737600-1738400	Genic enhancers	Gastric	stomach
45	chr6:1737800-1738400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr6:1737800-1738400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:1737800-1738400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
48	chr6:1737800-1738400	ZNF genes & repeats	Fetal Kidney	kidney
49	chr6:1737800-1738400	Genic enhancers	Pancreas	Pancrea
50	chr6:1738000-1740000	Enhancers	Spleen	Spleen

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