Variant report

Variant	esv3503365
Chromosome Location	chr6:128826884-128830707
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:128827840..128829694-chr6:128832240..128833795,2	MCF-7	breast:
2	chr2:197765766..197767854-chr6:128830235..128832178,2	MCF-7	breast:
3	chr6:128817873..128822661-chr6:128826854..128830658,5	MCF-7	breast:
4	chr6:128829914..128831519-chr6:128915307..128916935,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LAMA2-2	chr6:128827139-128827421	ENSG00000227112.1

Variant related genes	Relation type
ENSG00000224733	chromatin interactions

Extended variants
information (count: 150 )
Associated
traits (count: 98 )

Variant overlapped rSNPs/rCNVs (count:150 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs117686672	chr6:128826986-128826987	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs116034482	chr6:128826995-128826996	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs562711278	chr6:128827022-128827023	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs138475495	chr6:128827023-128827024	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs576904040	chr6:128827025-128827026	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs34931647	chr6:128827054-128827055	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs562355109	chr6:128827056-128827057	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs529659812	chr6:128827105-128827106	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs143009947	chr6:128827134-128827135	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs527326779	chr6:128827158-128827159	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs200878647	chr6:128827183-128827184	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
12	rs35803771	chr6:128827187-128827188	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
13	rs543745685	chr6:128827188-128827189	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
14	rs527964448	chr6:128827205-128827206	Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
15	rs191171973	chr6:128827207-128827208	Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
16	rs113057954	chr6:128827218-128827219	Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
17	rs563131637	chr6:128827276-128827277	Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
18	rs144313997	chr6:128827289-128827290	Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
19	rs11755787	chr6:128827310-128827311	Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
20	rs549004290	chr6:128827316-128827317	Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
21	rs148746447	chr6:128827370-128827371	Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
22	rs568376768	chr6:128827448-128827449	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs182906117	chr6:128827461-128827462	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs554183214	chr6:128827517-128827518	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs187340608	chr6:128827520-128827521	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs534069310	chr6:128827546-128827547	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs192126724	chr6:128827646-128827647	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs184379853	chr6:128827650-128827651	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs543990969	chr6:128827674-128827675	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs187527052	chr6:128827761-128827762	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs556198097	chr6:128827763-128827764	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs574176800	chr6:128827776-128827777	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs541459489	chr6:128827789-128827790	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs75484715	chr6:128827827-128827828	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs192404141	chr6:128827869-128827870	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs367592161	chr6:128827887-128827888	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs567160506	chr6:128827919-128827920	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs546043162	chr6:128828053-128828054	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs564532492	chr6:128828065-128828066	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs117423430	chr6:128828178-128828179	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs550028072	chr6:128828185-128828186	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs185823577	chr6:128828243-128828244	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs1016015	chr6:128828268-128828269	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs189079349	chr6:128828278-128828279	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs566074915	chr6:128828327-128828328	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs181071291	chr6:128828336-128828337	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs184700767	chr6:128828352-128828353	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs117776212	chr6:128828372-128828373	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs576353468	chr6:128828398-128828399	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs78918817	chr6:128828410-128828411	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:98)

Disease	PMID	Source
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Biliary cancer	19435499	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	21448237	CNVD
Autism	22495311	CNVD
Gastric cancer	17908304	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Neuroblastoma	18923191	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Melanoma	18172304	CNVD
Cancer	21637783	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
T-cell lymphomas	19863542	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	19010834	CNVD
Non-small cell lung cancer	21044232	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Hepatocellular carcinoma	22174799	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	16608533	CNVD
Non-small cell lung cancer	21385341	CNVD
Prostate cancer	16705090	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Ependymoma	16718352	CNVD
High-proliferative meningiomas	17937814	CNVD
Intracranial tumor	16823260	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	16272173	CNVD
Prostate cancer	18632612	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Urothelial carcinoma	18382360	CNVD
Ovarian neoplasms	16753589	CNVD
Hepatocellular carcinoma	16750200	CNVD
Wilms tumour	21544195	CNVD
Prostate cancer	19242612	CNVD
Glioma	21046410	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Zellweger syndrome	21572526	CNVD
Follicular lymphoma	20505157	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Malignant melanoma	18718029	CNVD
Lung adenocarcinoma	21935476	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21858162	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	17603634	CNVD
Chondromyxoid Fibroma	20696777	CNVD
Cancer	21183584	CNVD
Developmental delay	19490664	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Burkitt''s lymphoma	18698080	CNVD
Breast cancer	21785460	CNVD
Neurocytoma	17123091	CNVD
Chordoma	21602918	CNVD
Kartagener syndrome	16639409	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	17133270	CNVD
Follicular lymphoma	18703704	CNVD
Neurodevelopmental disorder	22521361	CNVD
small cell lung cancer	20016488	CNVD
Metastatic melanoma	18483359	CNVD
Adenoid cystic carcinoma	18698036	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Leukemia	18688285	CNVD
Ependymoma	18628472	CNVD
Ewing''s sarcoma	18628472	CNVD
Leukemia	18628472	CNVD
Breast cancer	21958427	CNVD
Mental retardation	17847001	CNVD
Cancer	17440070	CNVD
Myelofibrosis	22110671	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Breast cancer	21364760	CNVD
Glioblastoma multiforme	21390271	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:283 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128808800-128830800	Weak transcription	Lung	lung
2	chr6:128813000-128828600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:128815200-128833800	Enhancers	Fetal Intestine Large	intestine
4	chr6:128817200-128828600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:128817200-128839800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:128817200-128839800	Weak transcription	Aorta	Aorta
7	chr6:128819600-128827600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:128819800-128828600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:128819800-128828600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:128820600-128833800	Enhancers	Fetal Intestine Small	intestine
11	chr6:128820800-128828400	Weak transcription	HSMMtube	muscle
12	chr6:128820800-128828600	Weak transcription	HSMM	muscle
13	chr6:128821600-128836800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr6:128821800-128827000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:128821800-128827200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr6:128822000-128827000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr6:128822000-128828600	Weak transcription	Colonic Mucosa	Colon
18	chr6:128822200-128828600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:128822200-128828600	Weak transcription	Gastric	stomach
20	chr6:128822400-128828600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:128823400-128832800	Enhancers	Stomach Mucosa	stomach
22	chr6:128824400-128828600	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr6:128824600-128827200	Enhancers	Brain Substantia Nigra	brain
24	chr6:128824800-128829400	Enhancers	Fetal Heart	heart
25	chr6:128825000-128827200	Enhancers	Fetal Stomach	stomach
26	chr6:128825000-128827800	Enhancers	Brain Anterior Caudate	brain
27	chr6:128825000-128829400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:128825200-128827400	Enhancers	Colon Smooth Muscle	Colon
29	chr6:128825400-128828600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:128825600-128827000	Enhancers	NHDF-Ad	bronchial
31	chr6:128825600-128827400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:128825600-128827400	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr6:128825600-128827400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:128825600-128827800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:128825600-128828600	Enhancers	Muscle Satellite Cultured Cells	--
36	chr6:128825800-128827000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:128825800-128827200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr6:128825800-128828600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:128825800-128828600	Weak transcription	Small Intestine	intestine
40	chr6:128825800-128829800	Enhancers	Brain Hippocampus Middle	brain
41	chr6:128825800-128831200	Weak transcription	Psoas Muscle	Psoas
42	chr6:128825800-128832400	Weak transcription	Fetal Kidney	kidney
43	chr6:128825800-128840000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:128826000-128827200	Enhancers	HUVEC	blood vessel
45	chr6:128826000-128828200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr6:128826000-128828200	Weak transcription	NHEK	skin
47	chr6:128826000-128828600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:128826000-128828600	Weak transcription	Ovary	ovary
49	chr6:128826000-128828600	Weak transcription	Pancreas	Pancrea
50	chr6:128826000-128828600	Weak transcription	NH-A	brain

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