Variant report

Variant	nsv528405
Chromosome Location	chr12:103896595-103901502
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr12:103898904-103899904	GM12878	blood:	n/a	n/a
2	ATF2	chr12:103898900-103900028	GM12878	blood:	n/a	n/a
3	BATF	chr12:103899109-103899745	GM12878	blood:	n/a	chr12:103899555-103899564
4	BATF	chr12:103899033-103899891	GM12878	blood:	n/a	chr12:103899555-103899564
5	BCL11A	chr12:103898930-103899884	GM12878	blood:	n/a	n/a
6	BCL11A	chr12:103899055-103899814	GM12878	blood:	n/a	n/a
7	BCL3	chr12:103898971-103899862	GM12878	blood:	n/a	n/a
8	BCL3	chr12:103898980-103899861	GM12878	blood:	n/a	n/a
9	BCLAF1	chr12:103898965-103899956	GM12878	blood:	n/a	n/a
10	BCLAF1	chr12:103898983-103899887	GM12878	blood:	n/a	n/a
11	BHLHE40	chr12:103898972-103899935	GM12878	blood:	n/a	chr12:103899539-103899548 chr12:103899537-103899550 chr12:103899533-103899554 chr12:103899539-103899548
12	BRCA1	chr12:103899169-103899678	GM12878	blood:	n/a	n/a
13	CEBPB	chr12:103898908-103899987	GM12878	blood:	n/a	n/a
14	CEBPB	chr12:103899081-103899469	GM12878	blood:	n/a	n/a
15	CHD1	chr12:103898090-103898183	GM12878	blood:	n/a	n/a
16	CHD1	chr12:103898962-103900025	GM12878	blood:	n/a	n/a
17	CHD2	chr12:103898159-103898294	GM12878	blood:	n/a	n/a
18	CHD2	chr12:103898928-103899968	GM12878	blood:	n/a	n/a
19	CHD2	chr12:103897783-103897946	HepG2	liver:	n/a	n/a
20	CREB1	chr12:103899060-103899939	GM12878	blood:	n/a	n/a
21	CTCF	chr12:103897800-103897950	GM12866	blood:	n/a	chr12:103897866-103897875 chr12:103897862-103897875 chr12:103897860-103897878
22	CTCF	chr12:103897780-103897930	WERI-Rb-1	eye:	n/a	chr12:103897866-103897875 chr12:103897862-103897875 chr12:103897860-103897878
23	CTCF	chr12:103899400-103899550	GM12865	blood:	n/a	chr12:103899424-103899437 chr12:103899428-103899437 chr12:103899492-103899501
24	CTCF	chr12:103897777-103897963	Pancreas_OC	pancreas:	n/a	chr12:103897866-103897875 chr12:103897862-103897875 chr12:103897860-103897878
25	CTCF	chr12:103899460-103899610	GM12870	blood:	n/a	chr12:103899492-103899501
26	CTCF	chr12:103897651-103898091	MCF-7	breast:	n/a	chr12:103897723-103897731 chr12:103897866-103897875 chr12:103897862-103897875 chr12:103897860-103897878
27	CTCF	chr12:103897784-103897996	A549	lung:	n/a	chr12:103897866-103897875 chr12:103897862-103897875 chr12:103897860-103897878
28	CTCF	chr12:103899400-103899550	GM12866	blood:	n/a	chr12:103899424-103899437 chr12:103899428-103899437 chr12:103899492-103899501
29	CTCF	chr12:103897820-103897970	GM12873	blood:	n/a	chr12:103897866-103897875 chr12:103897862-103897875 chr12:103897860-103897878
30	CTCF	chr12:103897760-103897910	Caco-2	colon:	n/a	chr12:103897866-103897875 chr12:103897862-103897875 chr12:103897860-103897878
31	CTCF	chr12:103898180-103898330	GM12878	blood:	n/a	n/a
32	CTCF	chr12:103899460-103899610	GM12868	blood:	n/a	chr12:103899492-103899501
33	CTCF	chr12:103897780-103897930	HCT-116	colon:	n/a	chr12:103897866-103897875 chr12:103897862-103897875 chr12:103897860-103897878
34	CTCF	chr12:103897812-103897980	Fibrobl	skin:	n/a	chr12:103897866-103897875 chr12:103897862-103897875 chr12:103897860-103897878
35	CTCF	chr12:103897800-103897950	NB4	blood:	n/a	chr12:103897866-103897875 chr12:103897862-103897875 chr12:103897860-103897878
36	CTCF	chr12:103897720-103897870	NHEK	skin:	n/a	chr12:103897723-103897731
37	CTCF	chr12:103897625-103898069	H1-hESC	embryonic stem cell:	n/a	chr12:103897723-103897731 chr12:103897866-103897875 chr12:103897862-103897875 chr12:103897860-103897878
38	CTCF	chr12:103897795-103897959	SK-N-SH_RA	brain:	n/a	chr12:103897866-103897875 chr12:103897862-103897875 chr12:103897860-103897878
39	CTCF	chr12:103897760-103897910	GM12868	blood:	n/a	chr12:103897866-103897875 chr12:103897862-103897875 chr12:103897860-103897878
40	CTCF	chr12:103899420-103899570	GM12873	blood:	n/a	chr12:103899424-103899437 chr12:103899428-103899437 chr12:103899492-103899501
41	CTCF	chr12:103897800-103897950	GM12873	blood:	n/a	chr12:103897866-103897875 chr12:103897862-103897875 chr12:103897860-103897878
42	CTCF	chr12:103897739-103898055	GM19239	blood:	n/a	chr12:103897866-103897875 chr12:103897862-103897875 chr12:103897860-103897878
43	CTCF	chr12:103897740-103897890	K562	blood:	n/a	chr12:103897866-103897875 chr12:103897862-103897875 chr12:103897860-103897878
44	CTCF	chr12:103899420-103899570	GM12868	blood:	n/a	chr12:103899424-103899437 chr12:103899428-103899437 chr12:103899492-103899501
45	CTCF	chr12:103897780-103897930	HEEpiC	esophagus:	n/a	chr12:103897866-103897875 chr12:103897862-103897875 chr12:103897860-103897878
46	CTCF	chr12:103897820-103897970	HVMF	connective:	n/a	chr12:103897866-103897875 chr12:103897862-103897875 chr12:103897860-103897878
47	CTCF	chr12:103897760-103897910	HCT-116	colon:	n/a	chr12:103897866-103897875 chr12:103897862-103897875 chr12:103897860-103897878
48	CTCF	chr12:103897820-103897970	HFF	foreskin:	n/a	chr12:103897866-103897875 chr12:103897862-103897875 chr12:103897860-103897878
49	CTCF	chr12:103899380-103899530	RPTEC	kidney:	n/a	chr12:103899424-103899437 chr12:103899428-103899437 chr12:103899492-103899501
50	CTCF	chr12:103899460-103899610	HMEC	breast:	n/a	chr12:103899492-103899501

No.	Distal block	Cell Line	Cell type
1	chr12:103343745..103344702-chr12:103897389..103898552,4	MCF-7	breast:
2	chr12:103719744..103720561-chr12:103897421..103897994,2	MCF-7	breast:
3	chr12:103342772..103343296-chr12:103897586..103898267,2	MCF-7	breast:
4	chr12:103794502..103795818-chr12:103897463..103898386,6	MCF-7	breast:
5	chr12:103900419..103903095-chr12:103904941..103907379,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C12orf42-4	chr12:103899762-103899952	NONHSAT030376
2	lnc-C12orf42-4	chr12:103899189-103899392	NONHSAT030376

Variant related genes	Relation type
ENSG00000257415	TF binding region
ENSG00000257994	TF binding region
ENSG00000171759	chromatin interactions

Extended variants
information (count: 164 )
Associated
traits (count: 67 )

Variant overlapped rSNPs/rCNVs (count:164 , 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	rs17034027	chr12:103896595-103896596	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs17034029	chr12:103896685-103896686	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs193125860	chr12:103896750-103896751	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs557383410	chr12:103896751-103896752	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs577068303	chr12:103896761-103896762	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs369515643	chr12:103896811-103896812	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs577326367	chr12:103896852-103896853	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs185618863	chr12:103896868-103896869	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs189330175	chr12:103896914-103896915	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs573606645	chr12:103896949-103896950	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs544468334	chr12:103896960-103896961	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs138079500	chr12:103896971-103896972	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs560033373	chr12:103896998-103896999	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs573352948	chr12:103897086-103897087	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs545621963	chr12:103897087-103897088	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs7139385	chr12:103897139-103897140	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs142693695	chr12:103897211-103897212	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs550968475	chr12:103897225-103897226	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs561104103	chr12:103897229-103897230	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs530142613	chr12:103897248-103897249	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs548998404	chr12:103897268-103897269	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs111653960	chr12:103897269-103897270	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs79570689	chr12:103897287-103897288	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs142775778	chr12:103897293-103897294	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs570982056	chr12:103897294-103897295	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs191411481	chr12:103897314-103897315	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs556670099	chr12:103897315-103897316	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs75356146	chr12:103897360-103897361	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs559706667	chr12:103897466-103897467	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs536289995	chr12:103897470-103897471	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs144260415	chr12:103897482-103897483	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs573493118	chr12:103897508-103897509	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs545586990	chr12:103897509-103897510	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs554258842	chr12:103897546-103897547	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs575938723	chr12:103897547-103897548	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs544703802	chr12:103897558-103897559	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs529676185	chr12:103897579-103897580	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs148755547	chr12:103897581-103897582	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs574708085	chr12:103897582-103897583	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs540629771	chr12:103897613-103897614	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs375173915	chr12:103897630-103897631	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs117820907	chr12:103897638-103897639	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs528391702	chr12:103897723-103897724	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs559804786	chr12:103897777-103897778	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs75320294	chr12:103897778-103897779	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs141515749	chr12:103897785-103897786	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs114496824	chr12:103897880-103897881	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs184185687	chr12:103897885-103897886	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs567356490	chr12:103897893-103897894	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs140165975	chr12:103897894-103897895	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
Non-syndromic sensorineural hearing loss	18451855	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:103893600-103897200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:103893600-103897200	Weak transcription	HMEC	breast
3	chr12:103893600-103897400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:103894000-103898000	Weak transcription	GM12878-XiMat	blood
5	chr12:103895800-103898200	Enhancers	Thymus	Thymus
6	chr12:103897200-103897400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:103897200-103897800	Enhancers	Fetal Thymus	thymus
8	chr12:103897200-103898000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:103897200-103900000	Enhancers	HMEC	breast
10	chr12:103897400-103898600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:103897400-103899600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:103897600-103898000	Enhancers	Primary B cells from peripheral blood	blood
13	chr12:103898000-103898400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:103898000-103898600	Enhancers	GM12878-XiMat	blood
15	chr12:103898000-103899000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr12:103898400-103899800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:103898600-103899800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:103898600-103900000	Flanking Active TSS	GM12878-XiMat	blood
19	chr12:103898600-103900000	Enhancers	NHEK	skin
20	chr12:103899000-103899200	Enhancers	Primary B cells from peripheral blood	blood
21	chr12:103900000-103900200	Enhancers	GM12878-XiMat	blood

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