Variant report

Variant	nsv469478
Chromosome Location	chr12:75419718-75479379
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	ATF1	chr12:75471599-75471657	K562	blood:	n/a	n/a
2	BHLHE40	chr12:75446343-75446405	A549	lung:	n/a	n/a
3	BHLHE40	chr12:75442107-75442113	HepG2	liver:	n/a	n/a
4	CEBPB	chr12:75434399-75434463	HepG2	liver:	n/a	chr12:75434441-75434452
5	CEBPB	chr12:75436602-75436732	H1-hESC	embryonic stem cell:	n/a	chr12:75436637-75436650
6	CTCF	chr12:75452280-75452430	MCF-7	breast:	n/a	n/a
7	CTCF	chr12:75452087-75452335	GM12878	blood:	n/a	chr12:75452181-75452197 chr12:75452175-75452196 chr12:75452185-75452193
8	CTCF	chr12:75452120-75452270	HCPEpiC	choroid plexus:	n/a	chr12:75452181-75452197 chr12:75452175-75452196 chr12:75452185-75452193
9	CTCF	chr12:75452160-75452310	HRPEpiC	eye:	n/a	chr12:75452181-75452197 chr12:75452175-75452196 chr12:75452185-75452193
10	CTCF	chr12:75472720-75472870	GM06990	blood:	n/a	n/a
11	CTCF	chr12:75452140-75452290	RPTEC	kidney:	n/a	chr12:75452181-75452197 chr12:75452175-75452196 chr12:75452185-75452193
12	CTCF	chr12:75452180-75452330	HMEC	breast:	n/a	chr12:75452181-75452197 chr12:75452185-75452193
13	CTCF	chr12:75452114-75452409	MCF-7	breast:	n/a	chr12:75452181-75452197 chr12:75452175-75452196 chr12:75452185-75452193
14	CTCF	chr12:75452100-75452250	HRE	kidney:	n/a	chr12:75452181-75452197 chr12:75452175-75452196 chr12:75452185-75452193
15	CTCF	chr12:75452010-75452495	HCT-116	colon:	n/a	chr12:75452181-75452197 chr12:75452175-75452196 chr12:75452185-75452193
16	CTCF	chr12:75452120-75452411	MCF-7	breast:	n/a	chr12:75452181-75452197 chr12:75452175-75452196 chr12:75452185-75452193
17	CTCF	chr12:75452154-75452267	Hela-S3	cervix:	n/a	chr12:75452181-75452197 chr12:75452175-75452196 chr12:75452185-75452193
18	CTCF	chr12:75452020-75452170	HMEC	breast:	n/a	n/a
19	CTCF	chr12:75452130-75452247	HepG2	liver:	n/a	chr12:75452181-75452197 chr12:75452175-75452196 chr12:75452185-75452193
20	CTCF	chr12:75471998-75472046	GM20000	blood:	n/a	n/a
21	CTCF	chr12:75452240-75452390	MCF-7	breast:	n/a	n/a
22	CTCF	chr12:75452101-75452338	IMR90	lung:	n/a	chr12:75452181-75452197 chr12:75452175-75452196 chr12:75452185-75452193
23	CTCF	chr12:75452159-75452275	HUVEC	blood vessel:	n/a	chr12:75452181-75452197 chr12:75452175-75452196 chr12:75452185-75452193
24	E2F4	chr12:75448685-75448690	MCF10A-Er-Src	breast:	n/a	n/a
25	EBF1	chr12:75442092-75442120	GM12878	blood:	n/a	n/a
26	EP300	chr12:75440045-75440049	K562	blood:	n/a	n/a
27	EP300	chr12:75441537-75441549	GM12878	blood:	n/a	n/a
28	FAM48A	chr12:75445899-75445994	GM12878	blood:	n/a	n/a
29	FAM48A	chr12:75439051-75439158	GM12878	blood:	n/a	n/a
30	GATA2	chr12:75422226-75422535	SH-SY5Y	brain:	n/a	n/a
31	GATA2	chr12:75477948-75478170	K562	blood:	n/a	n/a
32	GATA3	chr12:75422264-75422352	SH-SY5Y	brain:	n/a	n/a
33	MAFF	chr12:75440004-75440204	HepG2	liver:	n/a	n/a
34	MAFF	chr12:75465828-75465955	HepG2	liver:	n/a	chr12:75465873-75465891
35	MAFF	chr12:75441701-75442023	HepG2	liver:	n/a	chr12:75441838-75441856
36	MAFK	chr12:75441708-75442013	HepG2	liver:	n/a	chr12:75441844-75441858 chr12:75441843-75441859 chr12:75441841-75441852 chr12:75441841-75441861 chr12:75441850-75441861
37	MAFK	chr12:75439936-75440250	HepG2	liver:	n/a	n/a
38	MAFK	chr12:75468916-75469057	HepG2	liver:	n/a	chr12:75468998-75469012
39	MAFK	chr12:75441689-75442021	HepG2	liver:	n/a	chr12:75441844-75441858 chr12:75441843-75441859 chr12:75441841-75441852 chr12:75441841-75441861 chr12:75441850-75441861
40	MAFK	chr12:75441725-75442004	IMR90	lung:	n/a	chr12:75441844-75441858 chr12:75441843-75441859 chr12:75441841-75441852 chr12:75441841-75441861 chr12:75441850-75441861
41	MAFK	chr12:75440083-75440096	HepG2	liver:	n/a	n/a
42	MAFK	chr12:75439976-75440174	IMR90	lung:	n/a	n/a
43	MAFK	chr12:75465897-75465962	HepG2	liver:	n/a	n/a
44	MAFK	chr12:75441792-75441924	K562	blood:	n/a	chr12:75441844-75441858 chr12:75441843-75441859 chr12:75441841-75441852 chr12:75441841-75441861 chr12:75441850-75441861
45	MAFK	chr12:75465754-75466030	HepG2	liver:	n/a	chr12:75465875-75465891 chr12:75465875-75465886 chr12:75465875-75465886 chr12:75465875-75465890 chr12:75465874-75465888 chr12:75465876-75465887
46	MXI1	chr12:75434839-75434885	H1-hESC	embryonic stem cell:	n/a	n/a
47	MYC	chr12:75436331-75436442	MCF-7	breast:	n/a	n/a
48	MYC	chr12:75444410-75444498	MCF-7	breast:	n/a	n/a
49	MYC	chr12:75439359-75439649	MCF10A-Er-Src	breast:	n/a	chr12:75439473-75439489
50	NFYA	chr12:75434668-75434755	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:75435362-75435412	Hepatocyte	liver:	n/a
2	chr12:75435362-75435412	HRE	kidney:	n/a
3	chr12:75435362-75435412	NHBE	bronchial:	n/a
4	chr12:75435362-75435412	AG10803	skin:	n/a
5	chr12:75435362-75435412	AG04450	lung:	fetal
6	chr12:75435362-75435412	HPAEpiC	pulmonary alveolar:	n/a
7	chr12:75435362-75435412	GM12878	blood:	n/a
8	chr12:75435362-75435412	ECC-1	luminal epithelium:	n/a
9	chr12:75435362-75435412	AG09309	skin:	n/a
10	chr12:75435362-75435412	GM19239	blood:	n/a
11	chr12:75435362-75435412	AoSMC	blood vessel:	n/a
12	chr12:75435362-75435412	RPTEC	kidney:	n/a
13	chr12:75435362-75435412	HRPEpiC	eye:	n/a
14	chr12:75435362-75435412	SK-N-MC	brain:	n/a
15	chr12:75435362-75435412	PANC-1	pancreas:	n/a
16	chr12:75435362-75435412	HCT-116	colon:	n/a
17	chr12:75435362-75435412	HepG2	liver:	n/a
18	chr12:75435362-75435412	HRCEpiC	kidney:	n/a
19	chr12:75435362-75435412	MCF-7	breast:	n/a
20	chr12:75435362-75435412	Jurkat	blood:	n/a
21	chr12:75435362-75435412	HAEpiC	amniotic membrane:	n/a
22	chr12:75435362-75435412	NT2-D1	testis:	n/a
23	chr12:75435362-75435412	MCF10A-Er-Src	breast:	n/a
24	chr12:75435362-75435412	A549	lung:	n/a
25	chr12:75435362-75435412	T-47D	breast:	n/a
26	chr12:75435362-75435412	NB4	blood:	n/a
27	chr12:75435362-75435412	NHDF-neo	bronchial:	n/a
28	chr12:75435362-75435412	AG09319	gingival:	n/a
29	chr12:75435362-75435412	HCM	heart:	n/a
30	chr12:75435362-75435412	CMK	blood:	n/a
31	chr12:75435362-75435412	ovcar-3	ovarian:	n/a
32	chr12:75435362-75435412	HEK293	kidney:	embryo
33	chr12:75435362-75435412	GM12891	blood:	n/a
34	chr12:75435362-75435412	SAEC	small airway:	n/a
35	chr12:75435362-75435412	Caco-2	colon:	n/a
36	chr12:75435362-75435412	Hela-S3	cervix:	n/a
37	chr12:75435362-75435412	ProgFib	skin:	n/a
38	chr12:75435362-75435412	HIPEpiC	eye:	n/a
39	chr12:75435362-75435412	K562	blood:	n/a
40	chr12:75435362-75435412	HNPCEpiC	eye:	n/a
41	chr12:75435362-75435412	U87	brain:	n/a
42	chr12:75435362-75435412	HEEpiC	esophagus:	n/a
43	chr12:75435362-75435412	BJ	skin:	n/a
44	chr12:75435362-75435412	GM06990	blood:	n/a
45	chr12:75435362-75435412	AG04449	skin:	fetal
46	chr12:75435362-75435412	HCF	heart:	n/a
47	chr12:75435362-75435412	HCPEpiC	choroid plexus:	n/a
48	chr12:75435362-75435412	PrEC	prostate:	n/a
49	chr12:75435362-75435412	PFSK-1	brain:	n/a
50	chr12:75435362-75435412	H1-hESC	embryonic stem cell:	embryo

No.	Distal block	Cell Line	Cell type
1	chr12:75082796..75083489-chr12:75451709..75452443,2	MCF-7	breast:
2	chr12:75424336..75426758-chr12:75436388..75438151,2	K562	blood:
3	chr12:75471106..75471647-chr12:75480652..75481167,2	MCF-7	breast:
4	chr12:75443458..75445239-chr12:75448407..75451297,2	MCF-7	breast:
5	chr12:75449527..75451079-chr12:75455433..75457461,2	MCF-7	breast:
6	chr10:125205389..125206272-chr12:75451784..75452560,2	MCF-7	breast:
7	chr12:75435528..75437912-chr12:75438665..75440854,2	K562	blood:
8	chr12:75449527..75451079-chr12:75455433..75457461,2	MCF-7	breast:
9	chr12:75472504..75474383-chr12:75575455..75577189,2	K562	blood:
10	chr12:75450802..75452995-chr12:75458776..75460677,2	MCF-7	breast:
11	chr12:75140910..75141773-chr12:75451603..75452321,3	MCF-7	breast:
12	chr12:75435528..75437912-chr12:75438665..75440854,2	K562	blood:
13	chr12:75450802..75452995-chr12:75458776..75460677,2	MCF-7	breast:
14	chr12:75358040..75360198-chr12:75422290..75423830,2	MCF-7	breast:
15	chr12:75424336..75426758-chr12:75436388..75438151,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLIPR1L1-2	chr12:75434738-75435132	NONHSAT029518
2	lnc-GLIPR1L1-2	chr12:75434738-75434922	ENSG00000257434.1
3	lnc-GLIPR1L1-4	chr12:75477994-75478144	l_680_chr12:75477806-75480269_testes
4	lnc-GLIPR1L1-4	chr12:75477807-75477928	l_680_chr12:75477806-75480269_testes
5	lnc-GLIPR1L1-2	chr12:75419754-75419984	ENSG00000257434.1
6	lnc-GLIPR1L1-2	chr12:75434738-75437150	ENSG00000257434.1
7	lnc-GLIPR1L1-2	chr12:75421835-75421869	NONHSAT029518
8	lnc-GLIPR1L1-2	chr12:75434738-75435052	ENSG00000257434.1
9	lnc-GLIPR1L1-2	chr12:75438258-75438573	ENSG00000257434.1
10	lnc-GLIPR1L1-2	chr12:75419767-75419984	ENSG00000257434.1

Variant related genes	Relation type
ENSG00000257434	TF binding region
KCNC2	TF binding region
ENSG00000257434	CpG island
KCNC2	CpG island
ENSG00000166006	chromatin interactions

Extended variants
information (count: 693 )
Associated
traits (count: 75 )

Variant overlapped rSNPs/rCNVs (count:693 , 50 per page) page: 1 2 3 4 5 6 7 ... 14

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs17114487	chr12:75419718-75419719	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs372820345	chr12:75419739-75419740	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs113658017	chr12:75419769-75419770	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs12296877	chr12:75419771-75419772	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs534733424	chr12:75419773-75419774	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
6	rs73181351	chr12:75419846-75419847	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs547242795	chr12:75419858-75419859	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
8	rs574891390	chr12:75419872-75419873	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
9	rs140893132	chr12:75419918-75419919	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
10	rs185127734	chr12:75419921-75419922	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
11	rs552246653	chr12:75419939-75419940	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
12	rs536499582	chr12:75419954-75419955	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
13	rs552307561	chr12:75421837-75421838	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
14	rs150691830	chr12:75421860-75421861	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
15	rs532336523	chr12:75421861-75421862	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
16	rs201035109	chr12:75434632-75434633	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs199649749	chr12:75434658-75434659	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs539987201	chr12:75434659-75434660	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs200582875	chr12:75434661-75434662	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs142202027	chr12:75434668-75434669	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs199574101	chr12:75434676-75434677	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs192778671	chr12:75434677-75434678	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs151145866	chr12:75434709-75434710	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs201817574	chr12:75434715-75434716	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs200064128	chr12:75434733-75434734	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs200802007	chr12:75434741-75434742	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs201571849	chr12:75434756-75434757	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs527323748	chr12:75434760-75434761	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
29	rs547069553	chr12:75434782-75434783	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs563886888	chr12:75434783-75434784	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
31	rs199933613	chr12:75434787-75434788	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs12315332	chr12:75434807-75434808	Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs202246346	chr12:75434808-75434809	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs199846475	chr12:75434816-75434817	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs201192704	chr12:75434837-75434838	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs202005987	chr12:75434840-75434841	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs200295579	chr12:75434843-75434844	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs376897370	chr12:75434844-75434845	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
39	rs201222192	chr12:75434846-75434847	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
40	rs570210088	chr12:75434850-75434851	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
41	rs201703988	chr12:75434852-75434853	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
42	rs200282154	chr12:75434876-75434877	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
43	rs201492860	chr12:75434896-75434897	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
44	rs373306032	chr12:75434899-75434900	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
45	rs373399937	chr12:75434903-75434904	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
46	rs199820365	chr12:75434914-75434915	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
47	rs184812218	chr12:75434927-75434928	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
48	rs201427286	chr12:75434946-75434947	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
49	rs199579079	chr12:75434957-75434958	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
50	rs200705198	chr12:75434990-75434991	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:75)

Disease	PMID	Source
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
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
Neurodevelopmental disorder	22521361	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
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
Cancer	16751803	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21390271	CNVD
Cancer	20164919	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	21785460	CNVD
Acute myeloid leukemia	21251322	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Burkitt''s lymphoma	20823134	CNVD
abnormal development	18461090	CNVD
Prostate cancer	18632612	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
craniofacial dysmorphism	21918468	CNVD
Breast cancer	17133270	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Breast cancer	22032731	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
Hodgkin''s lymphoma	18641027	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Urothelial cell carcinoma	18451213	CNVD
Myelofibrosis	22110671	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Breast cancer	21509527	CNVD
Breast cancer	21364760	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75434600-75436400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:75435200-75435800	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr12:75435400-75436200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:75435600-75436000	Enhancers	Liver	Liver
5	chr12:75436400-75436600	Enhancers	Liver	Liver
6	chr12:75441600-75442000	Weak transcription	Pancreas	Pancrea
7	chr12:75442000-75442200	ZNF genes & repeats	Pancreas	Pancrea
8	chr12:75442400-75444000	Enhancers	Liver	Liver
9	chr12:75456000-75456400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:75456400-75456800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:75456800-75457600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:75457400-75457800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:75474000-75474600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:75474200-75474600	Enhancers	Rectal Smooth Muscle	rectum
15	chr12:75474200-75474800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:75474600-75480000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr12:75478400-75480200	Enhancers	Colon Smooth Muscle	Colon
18	chr12:75479200-75480200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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