Variant report

Variant	esv3370026
Chromosome Location	chr4:98044823-98067071
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RAP1GDS1-5	chr4:98055751-98056210	ENSG00000253170

Extended variants
information (count: 943 )
Associated
traits (count: 78 )

Variant overlapped rSNPs/rCNVs (count:943 , 50 per page) page: 1 2 3 4 5 6 7 ... 19

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs72884351	chr4:98044846-98044847	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs577139258	chr4:98044865-98044866	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs10004925	chr4:98044871-98044872	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs72884353	chr4:98044900-98044901	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs373462930	chr4:98044902-98044903	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs184221971	chr4:98044913-98044914	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs9993126	chr4:98044973-98044974	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs546681255	chr4:98044987-98044988	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs10015575	chr4:98044991-98044992	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs117515322	chr4:98045014-98045015	Enhancers ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs546840175	chr4:98045036-98045037	Enhancers ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs373343183	chr4:98045057-98045058	Enhancers ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs546444326	chr4:98045065-98045066	Enhancers ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs571405322	chr4:98045066-98045067	Enhancers ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs375426623	chr4:98045075-98045076	Enhancers ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs550849759	chr4:98045103-98045104	Enhancers ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs376467882	chr4:98045135-98045136	Enhancers ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs569278123	chr4:98045184-98045185	Enhancers ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs536239682	chr4:98045197-98045198	Enhancers ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs555078707	chr4:98045200-98045201	Enhancers ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs370687156	chr4:98045205-98045206	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs9993378	chr4:98045222-98045223	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs534000211	chr4:98045271-98045272	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs558740275	chr4:98045272-98045273	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs367841128	chr4:98045283-98045284	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs188945116	chr4:98045284-98045285	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs10023781	chr4:98045320-98045321	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs556570010	chr4:98045360-98045361	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs575230790	chr4:98045375-98045376	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs542237536	chr4:98045465-98045466	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs76669423	chr4:98045476-98045477	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs572992342	chr4:98045485-98045486	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs140651846	chr4:98045583-98045584	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs181744553	chr4:98045584-98045585	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs532340560	chr4:98045587-98045588	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs550931619	chr4:98045682-98045683	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs546886475	chr4:98045702-98045703	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs28842582	chr4:98045733-98045734	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs28761187	chr4:98045739-98045740	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs186219427	chr4:98045764-98045765	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs28869280	chr4:98045786-98045787	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs28775982	chr4:98045795-98045796	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs552206280	chr4:98045798-98045799	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs144541164	chr4:98045813-98045814	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs2865764	chr4:98045828-98045829	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs2865763	chr4:98045861-98045862	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
47	rs28865368	chr4:98045864-98045865	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs374907080	chr4:98045869-98045870	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs540357199	chr4:98045880-98045881	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs77208703	chr4:98045906-98045907	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:78)

Disease	PMID	Source
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Medulloblastoma	21979893	CNVD
Neuroblastoma	18923191	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21858162	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	17603634	CNVD
Hepatocellular carcinoma	16750200	CNVD
Myxofibrosarcoma	16751306	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Parkinson disease	18923514	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Breast cancer	16272173	CNVD
Colorectal cancer	19359472	CNVD
Malignant mesothelioma	18160781	CNVD
Medulloblastoma	18056178	CNVD
Multiple myeloma	17077331	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Oral squamous cell carcinoma	17134496	CNVD
4q-syndrome	17576883	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Muscular dystrophy	21149563	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Cervical cancer	21062161	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Lung cancer	19208797	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21785460	CNVD
Myelodysplastic syndrome	21251322	CNVD
Lung cancer	18438408	CNVD
Cancer	22429812	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	18414403	CNVD
primary effusion lymphomas	17116491	CNVD
small cell lung cancer	20016488	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17133270	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Colorectal cancer	20459617	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Hirschsprung''s Disease	21712996	CNVD
Congenital anomalies of the kidney and urinary tract	20505237	CNVD
Breast cancer	17393978	CNVD
Ovarian cancer	21720365	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Esophageal cancer	21851588	CNVD
Cancer	19907438	CNVD
Prostate cancer	16573809	CNVD
Multiple myeloma	16616336	CNVD
Myelofibrosis	22110671	CNVD
Schizophrenia	19197363	CNVD
Melanoma	20688739	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:98043400-98045000	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr4:98043800-98048600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr4:98044800-98045200	Enhancers	H9 Cell Line	embryonic stem cell
4	chr4:98044800-98045200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:98044800-98045200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:98044800-98045200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:98044800-98045400	Enhancers	H1 Cell Line	embryonic stem cell
8	chr4:98045000-98045200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
9	chr4:98045000-98045200	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr4:98045000-98045200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:98045000-98045200	ZNF genes & repeats	Gastric	stomach
12	chr4:98045200-98046000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr4:98045200-98049600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:98045400-98046400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr4:98046000-98047800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
16	chr4:98046400-98047200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
17	chr4:98047200-98048600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr4:98047800-98049400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr4:98048400-98049000	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr4:98048600-98048800	Enhancers	H1 Cell Line	embryonic stem cell
21	chr4:98048600-98049000	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr4:98049400-98049800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
23	chr4:98049800-98051400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr4:98051400-98052600	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr4:98051600-98055600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr4:98052600-98053400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:98053400-98053800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr4:98053800-98055400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr4:98055400-98056000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:98055400-98057400	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr4:98055600-98055800	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr4:98055800-98056200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr4:98056200-98056600	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr4:98057400-98058000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:98058000-98062000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
36	chr4:98059000-98062000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:98059200-98059400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
38	chr4:98059800-98064600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:98060000-98061000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
40	chr4:98060400-98060600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
41	chr4:98060600-98062200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
42	chr4:98060800-98062400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr4:98061000-98061200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
44	chr4:98061000-98062000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr4:98061000-98062000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:98061000-98062000	Enhancers	NHEK	skin
47	chr4:98061200-98061400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:98061200-98065400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr4:98061800-98062600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
50	chr4:98062000-98062200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell

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