Variant report

Variant	nsv524064
Chromosome Location	chr12:104061597-104065846
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr12:104065637-104065669	HepG2	liver:	n/a	n/a
2	CTCF	chr12:104062580-104062730	GM12869	blood:	n/a	n/a
3	CTCF	chr12:104062360-104062510	GM12868	blood:	n/a	n/a
4	CTCF	chr12:104062320-104062470	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr12:104062380-104062530	GM12865	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:104063640-104063690	AoSMC	blood vessel:	n/a
2	chr12:104063640-104063690	Caco-2	colon:	n/a
3	chr12:104063640-104063690	MCF10A-Er-Src	breast:	n/a
4	chr12:104063640-104063690	A549	lung:	n/a
5	chr12:104063640-104063690	Hepatocyte	liver:	n/a
6	chr12:104063640-104063690	GM06990	blood:	n/a
7	chr12:104063640-104063690	HUVEC	blood vessel:	n/a
8	chr12:104063640-104063690	HEEpiC	esophagus:	n/a
9	chr12:104063640-104063690	CMK	blood:	n/a
10	chr12:104063640-104063690	ECC-1	luminal epithelium:	n/a
11	chr12:104063640-104063690	PANC-1	pancreas:	n/a
12	chr12:104063640-104063690	HEK293	kidney:	embryo
13	chr12:104063640-104063690	HMEC	breast:	n/a
14	chr12:104063640-104063690	ovcar-3	ovarian:	n/a
15	chr12:104063640-104063690	BE2_C	brain:	n/a
16	chr12:104063640-104063690	AG09309	skin:	n/a
17	chr12:104063640-104063690	Jurkat	blood:	n/a
18	chr12:104063640-104063690	HRE	kidney:	n/a
19	chr12:104063640-104063690	IMR90	lung:	fetal
20	chr12:104063640-104063690	T-47D	breast:	n/a
21	chr12:104063640-104063690	AG04450	lung:	fetal
22	chr12:104063640-104063690	H1-hESC	embryonic stem cell:	embryo
23	chr12:104063640-104063690	ProgFib	skin:	n/a
24	chr12:104063640-104063690	NB4	blood:	n/a
25	chr12:104063640-104063690	HCM	heart:	n/a
26	chr12:104063640-104063690	MCF-7	breast:	n/a
27	chr12:104063640-104063690	PFSK-1	brain:	n/a
28	chr12:104063640-104063690	HL-60	blood:	n/a
29	chr12:104063640-104063690	HRPEpiC	eye:	n/a
30	chr12:104063640-104063690	NHDF-neo	bronchial:	n/a
31	chr12:104063640-104063690	GM12891	blood:	n/a
32	chr12:104063640-104063690	RPTEC	kidney:	n/a
33	chr12:104063640-104063690	SK-N-MC	brain:	n/a
34	chr12:104063640-104063690	NH-A	brain:	n/a
35	chr12:104063640-104063690	NHBE	bronchial:	n/a
36	chr12:104063640-104063690	SKMC	muscle:	n/a
37	chr12:104063640-104063690	HPAEpiC	pulmonary alveolar:	n/a
38	chr12:104063640-104063690	U87	brain:	n/a
39	chr12:104063640-104063690	K562	blood:	n/a
40	chr12:104063640-104063690	LNCaP	prostate:	n/a
41	chr12:104063640-104063690	SK-N-SH	brain:	n/a
42	chr12:104063640-104063690	HIPEpiC	eye:	n/a
43	chr12:104063640-104063690	HAEpiC	amniotic membrane:	n/a
44	chr12:104063640-104063690	HCF	heart:	n/a
45	chr12:104063640-104063690	PrEC	prostate:	n/a
46	chr12:104063640-104063690	Hela-S3	cervix:	n/a
47	chr12:104063640-104063690	AG10803	skin:	n/a
48	chr12:104063640-104063690	BJ	skin:	n/a
49	chr12:104063640-104063690	SAEC	small airway:	n/a
50	chr12:104063640-104063690	HNPCEpiC	eye:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104061705..104063209-chr12:104063963..104066627,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

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

No data

Variant related genes	Relation type
ENSG00000257766	TF binding region
ENSG00000257766	CpG island
ENSG00000257766	chromatin interactions

Extended variants
information (count: 198 )
Associated
traits (count: 67 )

Variant overlapped rSNPs/rCNVs (count:198 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs7296829	chr12:104061597-104061598	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs556048600	chr12:104061602-104061603	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs576775711	chr12:104061618-104061619	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs574231541	chr12:104061639-104061640	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs541473551	chr12:104061678-104061679	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs79025347	chr12:104061709-104061710	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs189832692	chr12:104061718-104061719	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs182817082	chr12:104061729-104061730	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs536135861	chr12:104061783-104061784	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs561656537	chr12:104061793-104061794	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs831429	chr12:104061831-104061832	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
12	rs541065796	chr12:104061863-104061864	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs564764899	chr12:104061880-104061881	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs578180703	chr12:104061920-104061921	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs187893982	chr12:104061938-104061939	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs543765945	chr12:104061962-104061963	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs78913932	chr12:104061968-104061969	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs529494538	chr12:104062080-104062081	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs549443793	chr12:104062087-104062088	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs565878729	chr12:104062098-104062099	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs191313830	chr12:104062251-104062252	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs551316066	chr12:104062275-104062276	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs571317474	chr12:104062312-104062313	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs553644966	chr12:104062339-104062340	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs539315305	chr12:104062360-104062361	Weak transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
26	rs374562850	chr12:104062397-104062398	Weak transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs183501097	chr12:104062415-104062416	Weak transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs375065963	chr12:104062454-104062455	Weak transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
29	rs569810604	chr12:104062475-104062476	Weak transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs571959794	chr12:104062481-104062482	Weak transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
31	rs368071595	chr12:104062485-104062486	Weak transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs370182235	chr12:104062517-104062518	Weak transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs373723959	chr12:104062519-104062520	Weak transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs368701603	chr12:104062525-104062526	Weak transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs372294848	chr12:104062532-104062533	Weak transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs376833606	chr12:104062536-104062537	Weak transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs557744481	chr12:104062563-104062564	Weak transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs549350512	chr12:104062648-104062649	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs188505396	chr12:104062675-104062676	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs544074357	chr12:104062704-104062705	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs113248208	chr12:104062764-104062765	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs371000998	chr12:104062808-104062809	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs563864806	chr12:104062824-104062825	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs114094795	chr12:104062901-104062902	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs142599689	chr12:104062947-104062948	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs559524857	chr12:104062983-104062984	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs528526294	chr12:104062991-104062992	Weak transcription Enhancers Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
48	rs552787557	chr12:104063005-104063006	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
49	rs150990191	chr12:104063062-104063063	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
50	rs1965076	chr12:104063090-104063091	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

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:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104033200-104062200	Weak transcription	Spleen	Spleen
2	chr12:104059200-104061600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr12:104060000-104063400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:104060000-104063600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr12:104060000-104064000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:104060200-104061600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr12:104060200-104063000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:104060200-104063000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:104060200-104063200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:104060200-104063200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:104060200-104063200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:104060200-104063600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:104061000-104061600	Enhancers	Fetal Heart	heart
14	chr12:104061400-104063200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:104061600-104064000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:104062200-104062600	Genic enhancers	Spleen	Spleen
17	chr12:104062200-104063400	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr12:104062600-104063000	Strong transcription	Spleen	Spleen
19	chr12:104063000-104063200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:104063000-104064800	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr12:104063000-104067400	Weak transcription	Spleen	Spleen
22	chr12:104063200-104063400	Enhancers	H1 Cell Line	embryonic stem cell
23	chr12:104063200-104063600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:104063200-104064200	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr12:104063200-104064600	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr12:104063200-104064800	Enhancers	H9 Cell Line	embryonic stem cell
27	chr12:104063200-104064800	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr12:104063400-104063600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr12:104063400-104064000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr12:104063400-104064400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:104063400-104064800	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr12:104063600-104063800	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr12:104063600-104064400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:104063600-104064800	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr12:104063600-104064800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:104063800-104064000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr12:104063800-104064200	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr12:104063800-104064200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr12:104063800-104064600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:104064000-104064200	Enhancers	H1 Cell Line	embryonic stem cell
41	chr12:104064000-104064400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr12:104064000-104064400	Bivalent Enhancer	HepG2	liver
43	chr12:104064000-104064800	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr12:104064000-104072000	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr12:104064200-104064400	Enhancers	Fetal Intestine Large	intestine
46	chr12:104064400-104064800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr12:104064400-104065800	Weak transcription	Fetal Intestine Large	intestine
48	chr12:104064400-104067400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:104064400-104071000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:104064600-104071200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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