Variant report

Variant	esv3366706
Chromosome Location	chr4:15921154-15924552
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	chr4:15919905..15922253-chr4:15932751..15934628,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD38-4	chr4:15921122-15923370	NONHSAT095650
2	lnc-CD38-4	chr4:15923379-15924281	NONHSAT095650

Extended variants
information (count: 128 )
Associated
traits (count: 49 )

Variant overlapped rSNPs/rCNVs (count:128 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs536680531	chr4:15921218-15921219	Weak transcription Enhancers Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
2	rs74744793	chr4:15921220-15921221	Weak transcription Enhancers Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
3	rs534894219	chr4:15921241-15921242	Weak transcription Enhancers Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
4	rs534252859	chr4:15921325-15921326	Weak transcription Enhancers Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
5	rs553889195	chr4:15921361-15921362	Weak transcription Enhancers Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
6	rs573943925	chr4:15921387-15921388	Weak transcription Enhancers Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
7	rs542973638	chr4:15921416-15921417	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
8	rs11723486	chr4:15921471-15921472	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs374548521	chr4:15921498-15921499	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
10	rs576312694	chr4:15921517-15921518	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
11	rs545234536	chr4:15921518-15921519	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
12	rs565132025	chr4:15921523-15921524	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
13	rs527385390	chr4:15921578-15921579	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
14	rs34044449	chr4:15921642-15921643	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
15	rs568701289	chr4:15921644-15921645	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
16	rs377538010	chr4:15921694-15921695	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
17	rs190821919	chr4:15921698-15921699	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
18	rs529723470	chr4:15921709-15921710	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
19	rs6828211	chr4:15921748-15921749	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs532068070	chr4:15921753-15921754	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
21	rs536242603	chr4:15921762-15921763	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
22	rs570008644	chr4:15921767-15921768	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
23	rs532444693	chr4:15921769-15921770	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
24	rs76286065	chr4:15921898-15921899	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
25	rs552405262	chr4:15921921-15921922	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
26	rs140243891	chr4:15921934-15921935	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
27	rs534048238	chr4:15921958-15921959	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
28	rs181644360	chr4:15922011-15922012	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
29	rs562114655	chr4:15922032-15922033	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
30	rs555914925	chr4:15922037-15922038	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
31	rs373085179	chr4:15922042-15922043	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
32	rs184663620	chr4:15922060-15922061	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
33	rs373891359	chr4:15922109-15922110	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
34	rs28460848	chr4:15922123-15922124	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs556127669	chr4:15922142-15922143	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
36	rs576372286	chr4:15922160-15922161	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
37	rs200820377	chr4:15922196-15922197	Enhancers Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
38	rs188535765	chr4:15922214-15922215	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
39	rs369304005	chr4:15922215-15922216	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
40	rs181292290	chr4:15922232-15922233	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
41	rs185155181	chr4:15922234-15922235	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
42	rs190747588	chr4:15922235-15922236	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
43	rs181076481	chr4:15922246-15922247	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
44	rs559273720	chr4:15922273-15922274	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
45	rs112875384	chr4:15922276-15922277	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
46	rs574441307	chr4:15922343-15922344	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
47	rs2532066	chr4:15922354-15922355	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs563227865	chr4:15922364-15922365	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
49	rs114607345	chr4:15922374-15922375	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
50	rs374472599	chr4:15922405-15922406	Enhancers Flanking Active TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:49)

Disease	PMID	Source
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Breast cancer	21509527	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21858162	CNVD
small cell lung cancer	20016488	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
Breast cancer	17133270	CNVD
lymphocytic leukemia	21291569	CNVD
Breast cancer	16608533	CNVD
Non-small cell lung cancer	21829676	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15911600-15924000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:15913600-15924400	Enhancers	HMEC	breast
3	chr4:15915000-15921400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:15915400-15922000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:15916400-15921800	Weak transcription	Osteobl	bone
6	chr4:15916800-15921800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr4:15917000-15921200	Weak transcription	NH-A	brain
8	chr4:15918400-15923800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:15919600-15922200	Enhancers	A549	lung
10	chr4:15919800-15921400	Weak transcription	NHDF-Ad	bronchial
11	chr4:15920000-15921200	Flanking Active TSS	NHEK	skin
12	chr4:15920200-15921200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:15920600-15922200	Weak transcription	Hela-S3	cervix
14	chr4:15920600-15922400	Weak transcription	Stomach Mucosa	stomach
15	chr4:15920600-15923800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:15920600-15937600	Weak transcription	Esophagus	oesophagus
17	chr4:15920800-15921800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:15921000-15922200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr4:15921200-15921800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:15921200-15922400	Enhancers	NH-A	brain
21	chr4:15921200-15922400	Transcr. at gene 5' and 3'	NHEK	skin
22	chr4:15921400-15922800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:15921400-15923800	Enhancers	NHDF-Ad	bronchial
24	chr4:15921800-15922000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr4:15921800-15922000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:15921800-15922400	Enhancers	Osteobl	bone
27	chr4:15921800-15922600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr4:15921800-15923800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:15921800-15924000	Enhancers	NHLF	lung
30	chr4:15922000-15922400	Enhancers	Muscle Satellite Cultured Cells	--
31	chr4:15922000-15922600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:15922000-15923600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:15922000-15923600	Enhancers	HUVEC	blood vessel
34	chr4:15922000-15923800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:15922000-15923800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:15922000-15924400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:15922200-15922800	Flanking Active TSS	A549	lung
38	chr4:15922200-15923000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:15922200-15923600	Enhancers	Hela-S3	cervix
40	chr4:15922200-15924200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:15922400-15922600	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr4:15922400-15922600	Flanking Active TSS	NHEK	skin
43	chr4:15922400-15923000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr4:15922400-15923000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr4:15922400-15923000	Flanking Active TSS	NH-A	brain
46	chr4:15922400-15923000	Flanking Active TSS	Osteobl	bone
47	chr4:15922400-15923400	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr4:15922400-15923400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr4:15922400-15923400	Enhancers	Stomach Mucosa	stomach
50	chr4:15922400-15923400	Enhancers	HSMMtube	muscle

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