Variant report

Variant	esv3530263
Chromosome Location	chr14:79159029-79165792
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	chr14:79163820-79163970	Hela-S3	cervix:	n/a	chr14:79163887-79163908
2	CTCF	chr14:79163880-79164030	K562	blood:	n/a	chr14:79163887-79163908
3	CTCF	chr14:79164100-79164250	NHEK	skin:	n/a	n/a
4	CTCF	chr14:79163780-79163930	GM12869	blood:	n/a	chr14:79163887-79163908
5	CTCF	chr14:79163770-79164024	LNCaP	prostate:	n/a	chr14:79163887-79163908
6	CTCF	chr14:79163840-79163990	HA-sp	spinal cord:	n/a	chr14:79163887-79163908
7	CTCF	chr14:79163800-79163950	NHEK	skin:	n/a	chr14:79163887-79163908
8	CTCF	chr14:79163840-79163990	GM12865	blood:	n/a	chr14:79163887-79163908
9	CTCF	chr14:79163836-79163985	ProgFib	skin:	n/a	chr14:79163887-79163908
10	CTCF	chr14:79163800-79163950	GM12871	blood:	n/a	chr14:79163887-79163908
11	CTCF	chr14:79163800-79163950	HCT-116	colon:	n/a	chr14:79163887-79163908
12	CTCF	chr14:79163840-79163990	HVMF	connective:	n/a	chr14:79163887-79163908
13	CTCF	chr14:79163860-79164010	HepG2	liver:	n/a	chr14:79163887-79163908
14	CTCF	chr14:79163820-79163970	GM12873	blood:	n/a	chr14:79163887-79163908
15	CTCF	chr14:79163840-79163990	BJ	skin:	n/a	chr14:79163887-79163908
16	CTCF	chr14:79163840-79163990	Caco-2	colon:	n/a	chr14:79163887-79163908
17	CTCF	chr14:79163800-79163950	GM12874	blood:	n/a	chr14:79163887-79163908
18	CTCF	chr14:79163860-79164010	HEK293	kidney:	n/a	chr14:79163887-79163908
19	CTCF	chr14:79163800-79163950	NB4	blood:	n/a	chr14:79163887-79163908
20	CTCF	chr14:79163860-79164010	NHEK	skin:	n/a	chr14:79163887-79163908
21	CTCF	chr14:79163900-79164050	HFF-Myc	foreskin:	n/a	n/a
22	CTCF	chr14:79163860-79164010	BJ	skin:	n/a	chr14:79163887-79163908
23	CTCF	chr14:79163840-79163990	AG09309	skin:	n/a	chr14:79163887-79163908
24	CTCF	chr14:79163840-79163990	GM06990	blood:	n/a	chr14:79163887-79163908
25	CTCF	chr14:79163754-79163986	HepG2	liver:	n/a	chr14:79163887-79163908
26	CTCF	chr14:79163780-79163930	HCM	heart:	n/a	chr14:79163887-79163908
27	CTCF	chr14:79163800-79163950	NHLF	lung:	n/a	chr14:79163887-79163908
28	CTCF	chr14:79163708-79164100	GM12878	blood:	n/a	chr14:79163887-79163908
29	CTCF	chr14:79163820-79163970	HFF	foreskin:	n/a	chr14:79163887-79163908
30	CTCF	chr14:79163840-79163990	SAEC	small airway:	n/a	chr14:79163887-79163908
31	CTCF	chr14:79163820-79163970	NHDF-neo	bronchial:	n/a	chr14:79163887-79163908
32	CTCF	chr14:79163817-79164002	Gliobla	brain:	n/a	chr14:79163887-79163908
33	CTCF	chr14:79163762-79164040	HUVEC	blood vessel:	n/a	chr14:79163887-79163908
34	CTCF	chr14:79163840-79163990	NHDF-neo	bronchial:	n/a	chr14:79163887-79163908
35	CTCF	chr14:79163714-79164051	A549	lung:	n/a	chr14:79163887-79163908
36	CTCF	chr14:79163722-79164119	IMR90	lung:	n/a	chr14:79163887-79163908
37	CTCF	chr14:79163840-79163990	GM12867	blood:	n/a	chr14:79163887-79163908
38	CTCF	chr14:79163840-79163990	RPTEC	kidney:	n/a	chr14:79163887-79163908
39	CTCF	chr14:79163781-79163957	A549	lung:	n/a	chr14:79163887-79163908
40	CTCF	chr14:79163820-79163970	AG04449	skin:	n/a	chr14:79163887-79163908
41	CTCF	chr14:79163534-79164313	A549	lung:	n/a	chr14:79163887-79163908
42	CTCF	chr14:79164180-79164330	GM12873	blood:	n/a	n/a
43	CTCF	chr14:79163900-79163924	GM20000	blood:	n/a	n/a
44	CTCF	chr14:79163800-79163950	HepG2	liver:	n/a	chr14:79163887-79163908
45	CTCF	chr14:79163790-79164024	Hela-S3	cervix:	n/a	chr14:79163887-79163908
46	CTCF	chr14:79163774-79164044	Medullo	brain:	n/a	chr14:79163887-79163908
47	CTCF	chr14:79163820-79163970	AG09319	gingival:	n/a	chr14:79163887-79163908
48	CTCF	chr14:79163820-79163970	GM12864	blood:	n/a	chr14:79163887-79163908
49	CTCF	chr14:79163840-79163990	SK-N-SH_RA	brain:	n/a	chr14:79163887-79163908
50	CTCF	chr14:79163820-79163970	GM12872	blood:	n/a	chr14:79163887-79163908

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr14:79162188-79162238	GM12891	blood:	n/a
2	chr14:79162188-79162238	HRCEpiC	kidney:	n/a
3	chr14:79162188-79162238	U87	brain:	n/a
4	chr14:79162188-79162238	HCPEpiC	choroid plexus:	n/a
5	chr14:79162188-79162238	HL-60	blood:	n/a
6	chr14:79162188-79162238	GM12878	blood:	n/a
7	chr14:79162188-79162238	RPTEC	kidney:	n/a
8	chr14:79162188-79162238	NB4	blood:	n/a
9	chr14:79162188-79162238	LNCaP	prostate:	n/a
10	chr14:79162188-79162238	SK-N-MC	brain:	n/a
11	chr14:79162188-79162238	GM12892	blood:	n/a
12	chr14:79162188-79162238	T-47D	breast:	n/a
13	chr14:79162188-79162238	AG10803	skin:	n/a
14	chr14:79162188-79162238	PFSK-1	brain:	n/a
15	chr14:79162188-79162238	HIPEpiC	eye:	n/a
16	chr14:79162188-79162238	SK-N-SH_RA	brain:	n/a
17	chr14:79162188-79162238	ECC-1	luminal epithelium:	n/a
18	chr14:79162188-79162238	PANC-1	pancreas:	n/a
19	chr14:79162188-79162238	Jurkat	blood:	n/a
20	chr14:79162188-79162238	ProgFib	skin:	n/a
21	chr14:79162188-79162238	HRE	kidney:	n/a
22	chr14:79162188-79162238	HAEpiC	amniotic membrane:	n/a
23	chr14:79162188-79162238	Caco-2	colon:	n/a
24	chr14:79162188-79162238	AG09309	skin:	n/a
25	chr14:79162188-79162238	NH-A	brain:	n/a
26	chr14:79162188-79162238	NHBE	bronchial:	n/a
27	chr14:79162188-79162238	MCF10A-Er-Src	breast:	n/a
28	chr14:79162188-79162238	CMK	blood:	n/a
29	chr14:79162188-79162238	HCF	heart:	n/a
30	chr14:79162188-79162238	AG04449	skin:	fetal
31	chr14:79162188-79162238	BJ	skin:	n/a
32	chr14:79162188-79162238	SAEC	small airway:	n/a
33	chr14:79162188-79162238	A549	lung:	n/a
34	chr14:79162188-79162238	NHDF-neo	bronchial:	n/a
35	chr14:79162188-79162238	SK-N-SH	brain:	n/a
36	chr14:79162188-79162238	HRPEpiC	eye:	n/a
37	chr14:79162188-79162238	AoSMC	blood vessel:	n/a
38	chr14:79162188-79162238	AG09319	gingival:	n/a
39	chr14:79162188-79162238	AG04450	lung:	fetal
40	chr14:79162188-79162238	Hepatocyte	liver:	n/a
41	chr14:79162188-79162238	Hela-S3	cervix:	n/a
42	chr14:79162188-79162238	H1-hESC	embryonic stem cell:	embryo
43	chr14:79162188-79162238	HNPCEpiC	eye:	n/a
44	chr14:79162188-79162238	HepG2	liver:	n/a
45	chr14:79162188-79162238	HCM	heart:	n/a
46	chr14:79162188-79162238	HEEpiC	esophagus:	n/a
47	chr14:79162188-79162238	HMEC	breast:	n/a
48	chr14:79162188-79162238	IMR90	lung:	fetal
49	chr14:79162188-79162238	HUVEC	blood vessel:	n/a
50	chr14:79162188-79162238	BE2_C	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:78488036..78488630-chr14:79163630..79164376,2	K562	blood:
2	chr14:78630320..78630924-chr14:79163432..79164245,2	MCF-7	breast:
3	chr14:78914156..78915026-chr14:79163475..79164182,2	MCF-7	breast:
4	chr14:79064098..79065061-chr14:79163439..79164257,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNW1-2	chr14:79164218-79164465	ENSG00000258719.1
2	lnc-SNW1-2	chr14:79161664-79162115	ENSG00000258719.1

Variant related genes	Relation type
NRXN3	TF binding region
ENSG00000258719	TF binding region
NRXN3	CpG island
ENSG00000258719	CpG island

Extended variants
information (count: 166 )
Associated
traits (count: 72 )

Variant overlapped rSNPs/rCNVs (count:166 , 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	rs143532602	chr14:79159618-79159619	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
2	rs576142424	chr14:79159627-79159628	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs541917441	chr14:79159685-79159686	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs191234404	chr14:79159718-79159719	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs148040006	chr14:79159719-79159720	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs184991731	chr14:79159756-79159757	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs564611742	chr14:79161492-79161493	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs146874868	chr14:79161532-79161533	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs377068253	chr14:79161568-79161569	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs140744287	chr14:79161573-79161574	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs6574464	chr14:79161622-79161623	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs373765824	chr14:79161661-79161662	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs529186563	chr14:79161662-79161663	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs191047556	chr14:79161663-79161664	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs180743681	chr14:79161680-79161681	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
16	rs145618123	chr14:79161681-79161682	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
17	rs557529439	chr14:79161709-79161710	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
18	rs146551532	chr14:79161730-79161731	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
19	rs535130126	chr14:79161746-79161747	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
20	rs556319958	chr14:79161757-79161758	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
21	rs576266455	chr14:79161776-79161777	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
22	rs58355788	chr14:79161780-79161781	Inactive region	TF binding region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs140975427	chr14:79161811-79161812	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
24	rs572307697	chr14:79161888-79161889	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
25	rs150213566	chr14:79161889-79161890	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
26	rs186332804	chr14:79161891-79161892	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
27	rs138843125	chr14:79161896-79161897	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
28	rs576803374	chr14:79161910-79161911	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
29	rs536494861	chr14:79161922-79161923	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
30	rs190831530	chr14:79161959-79161960	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
31	rs182991846	chr14:79161976-79161977	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
32	rs563436455	chr14:79161991-79161992	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
33	rs529121722	chr14:79162031-79162032	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
34	rs549252540	chr14:79162035-79162036	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
35	rs149508385	chr14:79162050-79162051	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
36	rs528416705	chr14:79162051-79162052	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
37	rs551354186	chr14:79162061-79162062	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
38	rs571185269	chr14:79162065-79162066	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
39	rs188658170	chr14:79162074-79162075	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
40	rs556655641	chr14:79162093-79162094	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
41	rs569889491	chr14:79162100-79162101	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
42	rs531249288	chr14:79162109-79162110	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
43	rs146057244	chr14:79162112-79162113	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
44	rs138881474	chr14:79162133-79162134	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs191354376	chr14:79162199-79162200	Inactive region	TF binding region CpG island	1 gene(s)	Overlapped CNVs	n/a
46	rs183310882	chr14:79162201-79162202	Inactive region	TF binding region CpG island	1 gene(s)	Overlapped CNVs	n/a
47	rs558116586	chr14:79162241-79162242	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs142900826	chr14:79162272-79162273	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs187864074	chr14:79162294-79162295	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs563774526	chr14:79162300-79162301	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:72)

Disease	PMID	Source
Esophageal cancer	21851588	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
High-proliferative meningiomas	17937814	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Non-small cell lung cancer	21044232	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Melanoma	18172304	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Medulloblastoma	21979893	CNVD
Oral cancer	21386901	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Hepatocellular carcinoma	22174799	CNVD
Neuroblastoma	19435921	CNVD
Colorectal cancer	19359472	CNVD
Breast cancer	17899364	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Gastrointestinal stromal cancer	17535989	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Paraganglioma	17535989	CNVD
Pulmonary chondroma	17535989	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Renal cell carcinoma	21668985	CNVD
Chronic myeloid leukemia	20724749	CNVD
Wilms tumour	21544195	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Urothelial carcinoma	21177765	CNVD
Breast cancer	21858162	CNVD
Lung cancer	18438408	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Colorectal cancer	16272173	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Colorectal cancer	16774939	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Neuroblastoma	18923191	CNVD
Barrett''s syndrome	19417022	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Breast cancer	17133270	CNVD
Basal cell lymphoma	17053054	CNVD
cataract	16735990	CNVD
Hepatocellular carcinoma	16750200	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Multiple myeloma	17550852	CNVD
Glioblastoma multiforme	21922591	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	16608533	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Intracranial aneurysm	16715129	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
small cell lung cancer	20016488	CNVD
Developmental delay	21147756	CNVD
Breast cancer	21364760	CNVD
Bladder cancer	21909424	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Autism	22209245	CNVD
Prostate cancer	22553170	CNVD
Cancer	20164919	CNVD
Breast cancer	21509527	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	17603634	CNVD
Glioblastoma	21080181	CNVD

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:79159600-79159800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr14:79164000-79164800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr14:79164200-79164800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr14:79164200-79165000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr14:79164400-79165000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr14:79164400-79165000	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr14:79164800-79167600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr14:79165000-79176800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr14:79165000-79181000	Weak transcription	Brain Inferior Temporal Lobe	brain

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