Variant report

Variant	esv3365777
Chromosome Location	chr6:5045312-5045678
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPP40-1	chr6:5044719-5047759	XLOC_005592

Extended variants
information (count: 16 )
Associated
traits (count: 97 )

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs535934170	chr6:5045313-5045314	Weak transcription Strong transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
2	rs554253778	chr6:5045315-5045316	Weak transcription Strong transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
3	rs142448207	chr6:5045339-5045340	Weak transcription Strong transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
4	rs369974985	chr6:5045362-5045363	Weak transcription Strong transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
5	rs2793260	chr6:5045402-5045403	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs58909675	chr6:5045422-5045423	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs200663996	chr6:5045424-5045425	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
8	rs563415893	chr6:5045442-5045443	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
9	rs577049833	chr6:5045447-5045448	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
10	rs541343278	chr6:5045487-5045488	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
11	rs185438584	chr6:5045535-5045536	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs574790168	chr6:5045536-5045537	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
13	rs146616521	chr6:5045539-5045540	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
14	rs1771876	chr6:5045541-5045542	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	mRNA abundance
15	rs190036516	chr6:5045601-5045602	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
16	rs76886366	chr6:5045663-5045664	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:97)

Disease	PMID	Source
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
Lung cancer	18438408	CNVD
Bladder cancer	21909424	CNVD
Multiple myeloma	17550852	CNVD
Ewing''s sarcoma	17952124	CNVD
Breast cancer	21364760	CNVD
Chronic lymphocytic leukemia	21546498	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
Congenital anomalies of the kidney and urinary tract	18694510	CNVD
Nasopharyngeal cancer	22815911	CNVD
dysmorphism	22105932	CNVD
psychomotor delay	22105932	CNVD
Ovarian cancer	19193619	CNVD
Osteosarcoma	16790693	CNVD
Hepatocellular carcinoma	16750200	CNVD
Basal cell lymphoma	21115979	CNVD
Acute lymphoblastic leukemia	21339820	CNVD

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5027200-5047200	Weak transcription	Adipose Nuclei	Adipose
2	chr6:5033400-5046000	Weak transcription	Fetal Intestine Small	intestine
3	chr6:5033400-5048600	Weak transcription	Aorta	Aorta
4	chr6:5034800-5045600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr6:5034800-5047400	Weak transcription	Esophagus	oesophagus
6	chr6:5035000-5047400	Weak transcription	Primary B cells from cord blood	blood
7	chr6:5035400-5047800	Weak transcription	Primary B cells from peripheral blood	blood
8	chr6:5037000-5050800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:5037200-5046000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr6:5043000-5045600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:5043800-5048400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr6:5044000-5046600	Weak transcription	Ovary	ovary
13	chr6:5044800-5045600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:5044800-5045600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr6:5045000-5045600	Strong transcription	Primary hematopoietic stem cells	blood
16	chr6:5045200-5045600	Genic enhancers	Fetal Muscle Leg	muscle
17	chr6:5045200-5045800	Strong transcription	Primary T cells from cord blood	blood
18	chr6:5045200-5046400	Enhancers	Fetal Brain Male	brain
19	chr6:5045200-5046400	Enhancers	Fetal Brain Female	brain
20	chr6:5045200-5047000	Enhancers	Fetal Stomach	stomach
21	chr6:5045400-5045600	Active TSS	Fetal Lung	lung
22	chr6:5045600-5045800	Flanking Active TSS	Fetal Lung	lung
23	chr6:5045600-5046000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:5045600-5046000	Active TSS	Stomach Smooth Muscle	stomach
25	chr6:5045600-5046400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:5045600-5047000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr6:5045600-5047200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:5045600-5047200	Enhancers	Fetal Muscle Leg	muscle
29	chr6:5045600-5048400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr6:5045600-5048400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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