Variant report

Variant	esv3364343
Chromosome Location	chr15:75546999-75588597
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	ARID3A	chr15:75566765-75567085	HepG2	liver:	n/a	n/a
2	BATF	chr15:75571142-75571340	GM12878	blood:	n/a	n/a
3	BATF	chr15:75566750-75567078	GM12878	blood:	n/a	n/a
4	BCL11A	chr15:75575109-75575293	GM12878	blood:	n/a	n/a
5	BCL11A	chr15:75560181-75560352	GM12878	blood:	n/a	n/a
6	BCL11A	chr15:75578133-75578306	GM12878	blood:	n/a	n/a
7	BCL11A	chr15:75571092-75571384	GM12878	blood:	n/a	chr15:75571302-75571309
8	BCL11A	chr15:75584457-75584628	GM12878	blood:	n/a	n/a
9	BCL11A	chr15:75550815-75550962	GM12878	blood:	n/a	n/a
10	BCL11A	chr15:75553856-75554029	GM12878	blood:	n/a	n/a
11	CTCF	chr15:75566840-75566990	HFF	foreskin:	n/a	chr15:75566904-75566920 chr15:75566909-75566918 chr15:75566898-75566919 chr15:75566903-75566921
12	CTCF	chr15:75584299-75584798	A549	lung:	n/a	chr15:75584587-75584605 chr15:75584590-75584598
13	CTCF	chr15:75566920-75567070	AoAF	blood vessel:	n/a	n/a
14	CTCF	chr15:75566797-75567051	MCF-7	breast:	n/a	chr15:75566904-75566920 chr15:75566909-75566918 chr15:75566898-75566919 chr15:75566903-75566921
15	CTCF	chr15:75566797-75567060	LNCaP	prostate:	n/a	chr15:75566904-75566920 chr15:75566909-75566918 chr15:75566898-75566919 chr15:75566903-75566921
16	CTCF	chr15:75586082-75586430	A549	lung:	n/a	n/a
17	CTCF	chr15:75566920-75567070	HBMEC	blood vessel:	n/a	n/a
18	CTCF	chr15:75566625-75567091	K562	blood:	n/a	chr15:75566904-75566920 chr15:75566909-75566918 chr15:75566898-75566919 chr15:75566903-75566921
19	CTCF	chr15:75567100-75567250	GM12871	blood:	n/a	n/a
20	CTCF	chr15:75566920-75567070	NHEK	skin:	n/a	n/a
21	CTCF	chr15:75560094-75560453	A549	lung:	n/a	n/a
22	CTCF	chr15:75560269-75560409	LNCaP	prostate:	n/a	n/a
23	CTCF	chr15:75566580-75566730	HPF	lung:	n/a	n/a
24	CTCF	chr15:75560247-75560396	GM10266	blood:	n/a	n/a
25	CTCF	chr15:75584507-75584681	GM13976	blood:	n/a	chr15:75584587-75584605 chr15:75584590-75584598
26	CTCF	chr15:75566580-75566730	GM12864	blood:	n/a	n/a
27	CTCF	chr15:75560209-75560418	Pancreas_OC	pancreas:	n/a	n/a
28	CTCF	chr15:75566640-75566790	SK-N-SH_RA	brain:	n/a	n/a
29	CTCF	chr15:75566820-75566970	A549	lung:	n/a	chr15:75566904-75566920 chr15:75566909-75566918 chr15:75566898-75566919 chr15:75566903-75566921
30	CTCF	chr15:75568040-75568190	HepG2	liver:	n/a	n/a
31	CTCF	chr15:75586123-75586413	K562	blood:	n/a	n/a
32	CTCF	chr15:75567060-75567210	BE2_C	brain:	n/a	n/a
33	CTCF	chr15:75566580-75566730	GM12872	blood:	n/a	n/a
34	CTCF	chr15:75584517-75584685	Spleen_OC	spleen:	n/a	chr15:75584587-75584605 chr15:75584590-75584598
35	CTCF	chr15:75560210-75560429	GM13976	blood:	n/a	n/a
36	CTCF	chr15:75560267-75560390	Kidney_OC	kidney:	n/a	n/a
37	CTCF	chr15:75559908-75560630	A549	lung:	n/a	n/a
38	CTCF	chr15:75567120-75567270	SAEC	small airway:	n/a	n/a
39	CTCF	chr15:75584478-75584775	A549	lung:	n/a	chr15:75584587-75584605 chr15:75584590-75584598
40	CTCF	chr15:75566840-75566990	HMEC	breast:	n/a	chr15:75566904-75566920 chr15:75566909-75566918 chr15:75566898-75566919 chr15:75566903-75566921
41	CTCF	chr15:75566800-75566950	HepG2	liver:	n/a	chr15:75566904-75566920 chr15:75566909-75566918 chr15:75566898-75566919 chr15:75566903-75566921
42	CTCF	chr15:75566920-75567070	AG10803	skin:	n/a	n/a
43	CTCF	chr15:75560241-75560383	GM13977	blood:	n/a	n/a
44	CTCF	chr15:75566820-75566970	WI-38	lung:	n/a	chr15:75566904-75566920 chr15:75566909-75566918 chr15:75566898-75566919 chr15:75566903-75566921
45	CTCF	chr15:75566722-75567144	Gliobla	brain:	n/a	chr15:75566904-75566920 chr15:75566909-75566918 chr15:75566898-75566919 chr15:75566903-75566921
46	CTCF	chr15:75566800-75567048	Hela-S3	cervix:	n/a	chr15:75566904-75566920 chr15:75566909-75566918 chr15:75566898-75566919 chr15:75566903-75566921
47	CTCF	chr15:75566920-75567070	HUVEC	blood vessel:	n/a	n/a
48	CTCF	chr15:75567480-75567630	HCFaa	heart:	n/a	n/a
49	CTCF	chr15:75566697-75567137	K562	blood:	n/a	chr15:75566904-75566920 chr15:75566909-75566918 chr15:75566898-75566919 chr15:75566903-75566921
50	CTCF	chr15:75566920-75567070	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:75587027-75587077	HPAEpiC	pulmonary alveolar:	n/a
2	chr15:75587027-75587077	HPAEpiC	pulmonary alveolar:	n/a
3	chr15:75575161-75575211	A549	lung:	n/a
4	chr15:75575161-75575211	ECC-1	luminal epithelium:	n/a
5	chr15:75586717-75586767	RPTEC	kidney:	n/a
6	chr15:75586717-75586767	T-47D	breast:	n/a
7	chr15:75587027-75587077	AG09309	skin:	n/a
8	chr15:75587027-75587077	K562	blood:	n/a
9	chr15:75575161-75575211	BJ	skin:	n/a
10	chr15:75551123-75551173	NHBE	bronchial:	n/a
11	chr15:75586717-75586767	AoSMC	blood vessel:	n/a
12	chr15:75586717-75586767	AG04449	skin:	fetal
13	chr15:75551123-75551173	NHDF-neo	bronchial:	n/a
14	chr15:75551123-75551173	GM19239	blood:	n/a
15	chr15:75575161-75575211	GM12892	blood:	n/a
16	chr15:75575161-75575211	AG09309	skin:	n/a
17	chr15:75551123-75551173	Caco-2	colon:	n/a
18	chr15:75587027-75587077	ECC-1	luminal epithelium:	n/a
19	chr15:75587027-75587077	IMR90	lung:	fetal
20	chr15:75551123-75551173	CMK	blood:	n/a
21	chr15:75551123-75551173	HMEC	breast:	n/a
22	chr15:75586717-75586767	SK-N-MC	brain:	n/a
23	chr15:75551123-75551173	NB4	blood:	n/a
24	chr15:75551123-75551173	ovcar-3	ovarian:	n/a
25	chr15:75587027-75587077	HRCEpiC	kidney:	n/a
26	chr15:75586717-75586767	HEK293	kidney:	embryo
27	chr15:75587027-75587077	NHBE	bronchial:	n/a
28	chr15:75586717-75586767	HAEpiC	amniotic membrane:	n/a
29	chr15:75587027-75587077	MCF10A-Er-Src	breast:	n/a
30	chr15:75587027-75587077	H1-hESC	embryonic stem cell:	embryo
31	chr15:75575161-75575211	CMK	blood:	n/a
32	chr15:75575161-75575211	SAEC	small airway:	n/a
33	chr15:75575161-75575211	GM06990	blood:	n/a
34	chr15:75575161-75575211	NHDF-neo	bronchial:	n/a
35	chr15:75551123-75551173	LNCaP	prostate:	n/a
36	chr15:75587027-75587077	SK-N-SH	brain:	n/a
37	chr15:75575161-75575211	SK-N-SH	brain:	n/a
38	chr15:75551123-75551173	SK-N-SH	brain:	n/a
39	chr15:75575161-75575211	GM12878	blood:	n/a
40	chr15:75575161-75575211	RPTEC	kidney:	n/a
41	chr15:75586717-75586767	K562	blood:	n/a
42	chr15:75551123-75551173	HRE	kidney:	n/a
43	chr15:75587027-75587077	Jurkat	blood:	n/a
44	chr15:75575161-75575211	HUVEC	blood vessel:	n/a
45	chr15:75551123-75551173	BE2_C	brain:	n/a
46	chr15:75575161-75575211	HepG2	liver:	n/a
47	chr15:75575161-75575211	AG10803	skin:	n/a
48	chr15:75586717-75586767	HepG2	liver:	n/a
49	chr15:75586717-75586767	NB4	blood:	n/a
50	chr15:75586717-75586767	GM12891	blood:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75321592..75322142-chr15:75566565..75567153,2	MCF-7	breast:
2	chr15:74600289..74600861-chr15:75566666..75567634,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GOLGA6D-3	chr15:75560749-75561024	NONHSAT047302
2	lnc-MAN2C1-9	chr15:75564454-75564996	ncRnaDb_ncrna_FR096405_1
3	lnc-GOLGA6C-1	chr15:75585025-75585300	NONHSAT047303

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	GOLGA6A	hsa-miR-192-5p	chr15:75562833-75562852

Variant related genes	Relation type
GOLGA6D	TF binding region
NIFKP4	TF binding region
RN7SL489P	TF binding region
RN7SL327P	TF binding region
GOLGA6C	TF binding region
GOLGA6D	CpG island
NIFKP4	CpG island
RN7SL489P	CpG island
RN7SL327P	CpG island
GOLGA6C	CpG island

Extended variants
information (count: 230 )
Associated
traits (count: 67 )

Variant overlapped rSNPs/rCNVs (count:230 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs201120327	chr15:75547056-75547057	Inactive region	TF binding region	2 gene(s)	Overlapped CNVs	n/a
2	rs532786896	chr15:75547065-75547066	Inactive region	TF binding region	2 gene(s)	Overlapped CNVs	n/a
3	rs547652840	chr15:75547128-75547129	Inactive region	TF binding region	2 gene(s)	Overlapped CNVs	n/a
4	rs111542737	chr15:75547232-75547233	Inactive region	TF binding region	2 gene(s)	Overlapped CNVs	n/a
5	rs375140823	chr15:75547259-75547260	Inactive region	TF binding region	2 gene(s)	Overlapped CNVs	n/a
6	rs368107480	chr15:75547280-75547281	Inactive region	TF binding region	2 gene(s)	Overlapped CNVs	n/a
7	rs559830136	chr15:75547351-75547352	Inactive region	TF binding region	2 gene(s)	Overlapped CNVs	n/a
8	rs530150069	chr15:75547457-75547458	Inactive region	TF binding region	2 gene(s)	Overlapped CNVs	n/a
9	rs112080841	chr15:75547459-75547460	Inactive region	TF binding region	2 gene(s)	Overlapped CNVs	n/a
10	rs200490445	chr15:75550684-75550685	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs571546647	chr15:75550787-75550788	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs201328686	chr15:75556127-75556128	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs374912895	chr15:75556927-75556928	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs201887394	chr15:75557038-75557039	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs62027348	chr15:75557088-75557089	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs372600414	chr15:75557136-75557137	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs564326944	chr15:75557410-75557411	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs528446792	chr15:75557423-75557424	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs375714613	chr15:75557437-75557438	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs547415331	chr15:75557450-75557451	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs200390814	chr15:75557467-75557468	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs529865262	chr15:75557468-75557469	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs369021044	chr15:75557477-75557478	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs547965780	chr15:75557496-75557497	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs199815577	chr15:75557497-75557498	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs536769722	chr15:75557524-75557525	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs558572986	chr15:75557525-75557526	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs570359796	chr15:75557540-75557541	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs200780958	chr15:75557595-75557596	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs534610443	chr15:75557598-75557599	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs201970690	chr15:75557613-75557614	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs199745302	chr15:75557692-75557693	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs542509525	chr15:75557696-75557697	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs557611629	chr15:75557699-75557700	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs575862683	chr15:75557714-75557715	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs200701279	chr15:75557730-75557731	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs540599214	chr15:75558400-75558401	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs201074750	chr15:75558430-75558431	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs559421208	chr15:75558798-75558799	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs529952007	chr15:75558806-75558807	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs548050146	chr15:75558830-75558831	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs4104268	chr15:75560655-75560656	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs62027350	chr15:75560953-75560954	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
44	rs544294793	chr15:75564811-75564812	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
45	rs375268422	chr15:75564902-75564903	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
46	rs573833100	chr15:75566219-75566220	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs544331398	chr15:75566226-75566227	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs562430738	chr15:75566278-75566279	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs369822176	chr15:75566282-75566283	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs532988497	chr15:75566323-75566324	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:67)

Disease	PMID	Source
Ewing''s sarcoma	21437220	CNVD
Schizophrenia	19415332	CNVD
Breast cancer	22522925	CNVD
Wilms tumour	21544195	CNVD
Testicular germ cell tumor	18059402	CNVD
cataract	16735990	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Medulloblastoma	21979893	CNVD
spastic paraplegia with thinning of corpus callosum	19105190	CNVD
Schizophrenia	21324950	CNVD
Astrocytoma	17387387	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Disease	21824424	CNVD
Melanoma	18172304	CNVD
Gastric cancer	17167181	CNVD
Neuroblastoma	19435921	CNVD
Colorectal cancer	19359472	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Colorectal cancer	16272173	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Multiple myeloma	17550852	CNVD
Intellectual disability	22102821	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute myeloid leukemia	20729466	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Multiple myeloma	20724749	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Prostate cancer	18632612	CNVD
small cell lung cancer	20016488	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Cancer	16751803	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Breast cancer	17133270	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Autism	17322880	CNVD
phobic disorder	16773131	CNVD
Autism	21480499	CNVD
Disorders of sex development	22290220	CNVD
Mental retardation	19951919	CNVD
Mental retardation	16773131	CNVD
T-cell lymphomas	19863542	CNVD
15q24 microdeletion syndrome	22180641	CNVD
15q24 microdeletion syndrome	19921647	CNVD
Disease	22216833	CNVD
Mental retardation	17360722	CNVD
15q24 microdeletion syndrome	22216833	CNVD
15q24 microdeletion syndrome	22283845	CNVD
Developmental delay	17932688	CNVD
craniofacial dysmorphism	17932688	CNVD
digital and genital abnormalities	17932688	CNVD
Epilepsy	22083797	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Myelofibrosis	22110671	CNVD
Bipolar disorder	19114987	CNVD
Lung cancer	18438408	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Multiple myeloma	16616336	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75544600-75547000	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr15:75566200-75567200	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr15:75566400-75568000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:75566600-75567200	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr15:75566600-75567200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr15:75566800-75567200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr15:75566800-75567400	Enhancers	Liver	Liver
8	chr15:75567000-75567200	Enhancers	Spleen	Spleen
9	chr15:75567000-75567200	Bivalent Enhancer	HepG2	liver
10	chr15:75567000-75567400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:75567000-75567400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
12	chr15:75567000-75567600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:75567200-75568000	Weak transcription	Spleen	Spleen
14	chr15:75567200-75571000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr15:75567200-75571000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr15:75567600-75568000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:75568000-75568200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:75568000-75568400	Bivalent/Poised TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:75568000-75568400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:75568000-75568400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:75568000-75568400	Active TSS	Spleen	Spleen
22	chr15:75568200-75568400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:75570800-75571200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:75570800-75571200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:75570800-75571200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:75570800-75571200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:75571000-75571200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr15:75571000-75571200	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr15:75571000-75571200	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr15:75571000-75571200	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr15:75571000-75571200	Enhancers	HepG2	liver

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