Variant report

Variant	nsv869983
Chromosome Location	chr12:38598586-38664336
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	CTCF	chr12:38612760-38612910	HEEpiC	esophagus:	n/a	n/a
2	CTCF	chr12:38612805-38612900	SK-N-SH_RA	brain:	n/a	n/a
3	CTCF	chr12:38608187-38608207	Spleen_OC	spleen:	n/a	n/a
4	CTCF	chr12:38612760-38612910	HCT-116	colon:	n/a	n/a
5	CTCF	chr12:38630488-38630534	LNCaP	prostate:	n/a	n/a
6	CTCF	chr12:38612780-38612930	A549	lung:	n/a	n/a
7	CTCF	chr12:38612881-38612930	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr12:38612780-38612930	SK-N-SH_RA	brain:	n/a	n/a
9	CTCF	chr12:38600398-38600508	Medullo	brain:	n/a	n/a
10	CTCF	chr12:38612820-38612970	A549	lung:	n/a	n/a
11	CTCF	chr12:38660224-38660353	GM20000	blood:	n/a	n/a
12	CTCF	chr12:38612820-38612970	NHEK	skin:	n/a	n/a
13	CTCF	chr12:38637114-38637166	LNCaP	prostate:	n/a	n/a
14	CTCF	chr12:38612840-38612990	RPTEC	kidney:	n/a	n/a
15	CTCF	chr12:38612840-38612990	HEEpiC	esophagus:	n/a	n/a
16	CTCF	chr12:38612840-38612990	BE2_C	brain:	n/a	n/a
17	CTCF	chr12:38633694-38633745	GM10248	blood:	n/a	n/a
18	CTCF	chr12:38612820-38612970	HMEC	breast:	n/a	n/a
19	CTCF	chr12:38650686-38650740	GM20000	blood:	n/a	n/a
20	CTCF	chr12:38612840-38612990	Caco-2	colon:	n/a	n/a
21	CTCF	chr12:38612860-38613010	RPTEC	kidney:	n/a	n/a
22	CTCF	chr12:38612880-38613030	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr12:38612816-38612964	SK-N-SH_RA	brain:	n/a	n/a
24	CTCF	chr12:38612820-38612970	BE2_C	brain:	n/a	n/a
25	CTCF	chr12:38642375-38642418	A549	lung:	n/a	n/a
26	CTCF	chr12:38612880-38613030	Caco-2	colon:	n/a	n/a
27	CTCF	chr12:38600036-38600082	LNCaP	prostate:	n/a	n/a
28	E2F4	chr12:38618873-38618948	MCF10A-Er-Src	breast:	n/a	n/a
29	E2F4	chr12:38663881-38663939	MCF10A-Er-Src	breast:	n/a	n/a
30	ESR1	chr12:38610666-38611001	T-47D	breast:	n/a	n/a
31	ESR1	chr12:38628303-38628582	ECC-1	luminal epithelium:	n/a	n/a
32	ESR1	chr12:38628618-38628858	ECC-1	luminal epithelium:	n/a	n/a
33	ESR1	chr12:38610668-38610929	T-47D	breast:	n/a	n/a
34	ESR1	chr12:38610611-38611043	T-47D	breast:	n/a	n/a
35	ESR1	chr12:38610656-38611016	T-47D	breast:	n/a	n/a
36	ESR1	chr12:38628302-38628914	ECC-1	luminal epithelium:	n/a	n/a
37	ESR1	chr12:38628200-38628954	ECC-1	luminal epithelium:	n/a	n/a
38	ESR1	chr12:38610637-38611059	T-47D	breast:	n/a	n/a
39	ESR1	chr12:38663603-38663909	ECC-1	luminal epithelium:	n/a	chr12:38663708-38663725
40	FOS	chr12:38663685-38664066	MCF10A-Er-Src	breast:	n/a	chr12:38663845-38663856 chr12:38663844-38663851 chr12:38663844-38663852
41	FOS	chr12:38631867-38632482	MCF10A-Er-Src	breast:	n/a	chr12:38632356-38632364
42	FOS	chr12:38632080-38632551	MCF10A-Er-Src	breast:	n/a	chr12:38632356-38632364
43	FOS	chr12:38614507-38614707	MCF10A-Er-Src	breast:	n/a	n/a
44	FOS	chr12:38614571-38614660	MCF10A-Er-Src	breast:	n/a	n/a
45	FOS	chr12:38632122-38632452	MCF10A-Er-Src	breast:	n/a	chr12:38632356-38632364
46	FOS	chr12:38632089-38632450	MCF10A-Er-Src	breast:	n/a	chr12:38632356-38632364
47	FOS	chr12:38614572-38614707	MCF10A-Er-Src	breast:	n/a	n/a
48	FOS	chr12:38663746-38664033	MCF10A-Er-Src	breast:	n/a	chr12:38663845-38663856 chr12:38663844-38663851 chr12:38663844-38663852
49	FOS	chr12:38663700-38664044	MCF10A-Er-Src	breast:	n/a	chr12:38663845-38663856 chr12:38663844-38663851 chr12:38663844-38663852
50	FOS	chr12:38663699-38664070	MCF10A-Er-Src	breast:	n/a	chr12:38663845-38663856 chr12:38663844-38663851 chr12:38663844-38663852

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:38637847..38640659-chr12:38643822..38646474,2	K562	blood:
2	chr12:38637847..38640659-chr12:38643822..38646474,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CPNE8-6	chr12:38599188-38599814	NONHSAT027678

Variant related genes	Relation type
ENSG00000258360	TF binding region
ENSG00000257292	TF binding region

Extended variants
information (count: 2589 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:2589 , 50 per page) page: 1 2 3 4 5 6 7 ... 52

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs551642683	chr12:38598588-38598589	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs571424083	chr12:38598617-38598618	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs534081832	chr12:38598688-38598689	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs547684947	chr12:38598689-38598690	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs567288227	chr12:38598758-38598759	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs535904269	chr12:38598801-38598802	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs556105814	chr12:38598824-38598825	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs576105951	chr12:38598845-38598846	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs538718544	chr12:38598851-38598852	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs191011765	chr12:38598862-38598863	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs577770260	chr12:38598873-38598874	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs572576612	chr12:38598876-38598877	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs183813982	chr12:38598913-38598914	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs574251609	chr12:38598935-38598936	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs542701899	chr12:38598951-38598952	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs562891400	chr12:38598978-38598979	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs114071687	chr12:38599022-38599023	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs551849365	chr12:38599034-38599035	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs565097264	chr12:38599039-38599040	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs527446517	chr12:38599050-38599051	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs547600775	chr12:38599065-38599066	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs9919813	chr12:38599089-38599090	ZNF genes & repeats Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs536547115	chr12:38599095-38599096	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs562297007	chr12:38599163-38599164	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs146077418	chr12:38599169-38599170	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs569594713	chr12:38599211-38599212	ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs111812888	chr12:38599223-38599224	ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs538351033	chr12:38599237-38599238	ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
29	rs558203601	chr12:38599238-38599239	ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs73271997	chr12:38599255-38599256	ZNF genes & repeats Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs187944891	chr12:38599270-38599271	ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs553941345	chr12:38599291-38599292	ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs574293715	chr12:38599344-38599345	ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs543264548	chr12:38599366-38599367	ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs556284605	chr12:38599437-38599438	ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs138824077	chr12:38599475-38599476	ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs544864602	chr12:38599495-38599496	ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs565414436	chr12:38599503-38599504	ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
39	rs527765943	chr12:38599537-38599538	ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
40	rs541278001	chr12:38599541-38599542	ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
41	rs190587614	chr12:38599581-38599582	ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
42	rs201673302	chr12:38599583-38599584	ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
43	rs550002962	chr12:38599605-38599606	ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
44	rs183299297	chr12:38599617-38599618	ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
45	rs531948728	chr12:38599630-38599631	ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
46	rs113319357	chr12:38599634-38599635	ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
47	rs371072584	chr12:38599640-38599641	ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
48	rs150819811	chr12:38599665-38599666	ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
49	rs139213533	chr12:38599688-38599689	ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
50	rs9919778	chr12:38599719-38599720	ZNF genes & repeats	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:59)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Seminomas	18059402	CNVD
Wilms tumour	21544195	CNVD
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
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Neurodevelopmental disorder	22521361	CNVD
Breast cancer	21509527	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Renal cell carcinoma	18194544	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
Breast cancer	21364760	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	17603634	CNVD
Cancer	21183584	CNVD
Hirschsprung''s Disease	21712996	CNVD
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Acute myeloid leukemia	21251322	CNVD
small cell lung cancer	20016488	CNVD
Autism	20858243	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Autism	20531469	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:38594400-38600000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:38598200-38599600	Enhancers	Placenta	Placenta
3	chr12:38598400-38598800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:38599600-38599800	ZNF genes & repeats	Placenta	Placenta
5	chr12:38599800-38601200	Weak transcription	Placenta	Placenta
6	chr12:38601200-38601600	Enhancers	Placenta	Placenta
7	chr12:38604800-38614200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:38613200-38613400	Enhancers	Stomach Mucosa	stomach
9	chr12:38613600-38614600	Weak transcription	Stomach Mucosa	stomach
10	chr12:38614200-38615000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:38614200-38615000	Enhancers	HMEC	breast
12	chr12:38614600-38615800	Enhancers	Stomach Mucosa	stomach
13	chr12:38615000-38615400	Weak transcription	HMEC	breast
14	chr12:38615000-38615800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:38615400-38616200	Enhancers	HMEC	breast
16	chr12:38615800-38616400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:38616400-38631800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:38626800-38627600	Enhancers	HMEC	breast
19	chr12:38627600-38631600	Weak transcription	HMEC	breast
20	chr12:38628400-38628800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:38628800-38631400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:38631400-38633000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:38631600-38632600	Enhancers	HMEC	breast
24	chr12:38631800-38632400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:38640800-38641200	Active TSS	Fetal Heart	heart
26	chr12:38645600-38663800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:38654800-38655200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:38654800-38655800	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
29	chr12:38655200-38655600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:38655200-38655600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
31	chr12:38662400-38662800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:38662400-38662800	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr12:38663800-38664400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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