Variant report

Variant	nsv525838
Chromosome Location	chr12:104059790-104063090
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	chr12:104058121..104061173-chr12:104061276..104064386,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NT5DC3-2	chr12:104062990-104063184	ENSG00000257766.1
2	lnc-NT5DC3-2	chr12:104062353-104062625	ENSG00000257766.1

Variant related genes	Relation type
ENSG00000257766	chromatin interactions

Extended variants
information (count: 146 )
Associated
traits (count: 67 )

Variant overlapped rSNPs/rCNVs (count:146 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs755598	chr12:104059790-104059791	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs546261779	chr12:104059886-104059887	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs565175302	chr12:104059910-104059911	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs530779542	chr12:104059920-104059921	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs550860434	chr12:104059934-104059935	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs560884591	chr12:104059941-104059942	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs150900530	chr12:104060031-104060032	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs546354463	chr12:104060046-104060047	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs145341015	chr12:104060070-104060071	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs376165287	chr12:104060090-104060091	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs147674384	chr12:104060114-104060115	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs185800969	chr12:104060117-104060118	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs577289456	chr12:104060119-104060120	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs368817569	chr12:104060128-104060129	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs542357215	chr12:104060163-104060164	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs139392525	chr12:104060182-104060183	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs538123480	chr12:104060195-104060196	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs555267087	chr12:104060208-104060209	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs116547375	chr12:104060253-104060254	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs534440112	chr12:104060257-104060258	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs374905595	chr12:104060260-104060261	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs554299340	chr12:104060269-104060270	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs577460848	chr12:104060273-104060274	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs539671275	chr12:104060317-104060318	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs546323095	chr12:104060328-104060329	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs556523703	chr12:104060337-104060338	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs556556972	chr12:104060338-104060339	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs190477488	chr12:104060344-104060345	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs544149200	chr12:104060375-104060376	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs561261916	chr12:104060380-104060381	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs79691715	chr12:104060421-104060422	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs192365161	chr12:104060497-104060498	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs559810505	chr12:104060544-104060545	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs116123084	chr12:104060618-104060619	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs551872769	chr12:104060723-104060724	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs568486591	chr12:104060729-104060730	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs3752877	chr12:104060741-104060742	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs548585647	chr12:104060751-104060752	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs149645928	chr12:104060772-104060773	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs183656875	chr12:104060783-104060784	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs368930273	chr12:104060787-104060788	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs544009509	chr12:104060803-104060804	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs75134417	chr12:104060835-104060836	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs1809783	chr12:104060845-104060846	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs147127574	chr12:104060856-104060857	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs539907556	chr12:104060870-104060871	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs3752879	chr12:104060872-104060873	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs386765904	chr12:104060911-104060912	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs201512206	chr12:104060912-104060913	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs541410136	chr12:104060980-104060981	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:67)

Disease	PMID	Source
Esophageal cancer	21851588	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Ewing''s sarcoma	21437220	CNVD
Testicular germ cell tumor	18059402	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Autism	22495311	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	21949216	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21637783	CNVD
Glioblastoma multiforme	21080181	CNVD
Renal cell carcinoma	19461508	CNVD
Burkitt''s lymphoma	18698080	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Lung cancer	18438408	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21390271	CNVD
Cancer	20164919	CNVD
Breast cancer	22032731	CNVD
Cancer	16751803	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
Wilms tumour	21544195	CNVD
Ovarian cancer	21720365	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
lymphocytic leukemia	21291569	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17603634	CNVD
Breast cancer	16397240	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Sudden cardiac death	19188705	CNVD
Breast cancer	17133270	CNVD
Chronic lymphocytic leukemia	21049055	CNVD
Neurocytoma	17123091	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Breast cancer	21509527	CNVD
Breast cancer	21364760	CNVD
Multiple myeloma	16616336	CNVD
Myelofibrosis	22110671	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104033200-104062200	Weak transcription	Spleen	Spleen
2	chr12:104059200-104059800	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr12:104059200-104060000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:104059200-104060200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:104059200-104061600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr12:104059400-104060200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:104059600-104059800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:104059600-104060000	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr12:104059600-104060200	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr12:104059600-104060200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr12:104059600-104060200	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr12:104059600-104060200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:104059600-104060200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:104059600-104060400	Enhancers	H9 Cell Line	embryonic stem cell
15	chr12:104059800-104060000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:104059800-104060200	Enhancers	H1 Cell Line	embryonic stem cell
17	chr12:104060000-104060200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
18	chr12:104060000-104063400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:104060000-104063600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr12:104060000-104064000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:104060200-104061600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr12:104060200-104063000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:104060200-104063000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:104060200-104063200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr12:104060200-104063200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr12:104060200-104063200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr12:104060200-104063600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:104060400-104060800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr12:104060800-104061400	Enhancers	H9 Cell Line	embryonic stem cell
30	chr12:104061000-104061400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:104061000-104061600	Enhancers	Fetal Heart	heart
32	chr12:104061400-104063200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr12:104061600-104064000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr12:104062200-104062600	Genic enhancers	Spleen	Spleen
35	chr12:104062200-104063400	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr12:104062600-104063000	Strong transcription	Spleen	Spleen
37	chr12:104063000-104063200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:104063000-104064800	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr12:104063000-104067400	Weak transcription	Spleen	Spleen

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