Variant report

Variant	nsv517636
Chromosome Location	chr3:112878536-112893640
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:91)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:9)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:91 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr3:112884746-112884972	IMR90	lung:	n/a	n/a
2	CEBPB	chr3:112884730-112884994	H1-hESC	embryonic stem cell:	n/a	n/a
3	CEBPB	chr3:112884727-112884961	Hela-S3	cervix:	n/a	n/a
4	CEBPB	chr3:112892734-112892835	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr3:112888820-112888961	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr3:112888840-112888990	HEK293	kidney:	n/a	n/a
7	CTCF	chr3:112888920-112889070	GM12875	blood:	n/a	n/a
8	CTCF	chr3:112888820-112888970	GM12873	blood:	n/a	n/a
9	CTCF	chr3:112888880-112888885	Kidney_OC	kidney:	n/a	n/a
10	CTCF	chr3:112888800-112888950	GM12875	blood:	n/a	n/a
11	CTCF	chr3:112888780-112888930	WERI-Rb-1	eye:	n/a	n/a
12	CTCF	chr3:112888820-112888970	HepG2	liver:	n/a	n/a
13	CTCF	chr3:112885734-112885769	IMR90	lung:	n/a	n/a
14	CTCF	chr3:112888840-112888990	GM12864	blood:	n/a	n/a
15	CTCF	chr3:112888200-112888350	HCFaa	heart:	n/a	n/a
16	CTCF	chr3:112888700-112888850	HPAF	blood vessel:	n/a	n/a
17	CTCF	chr3:112888800-112888950	GM12865	blood:	n/a	n/a
18	CTCF	chr3:112886180-112886330	AG04449	skin:	n/a	n/a
19	CTCF	chr3:112888800-112888950	GM12871	blood:	n/a	n/a
20	CTCF	chr3:112888860-112889010	GM12873	blood:	n/a	n/a
21	EP300	chr3:112885366-112886577	ECC-1	luminal epithelium:	n/a	n/a
22	EP300	chr3:112885363-112886614	SK-N-SH	brain:	n/a	n/a
23	EP300	chr3:112885470-112885972	SK-N-SH_RA	brain:	n/a	n/a
24	EP300	chr3:112884726-112888406	SK-N-SH	brain:	n/a	chr3:112887213-112887226 chr3:112887094-112887108
25	EP300	chr3:112885979-112886481	SK-N-SH_RA	brain:	n/a	n/a
26	EP300	chr3:112885474-112886401	SK-N-SH_RA	brain:	n/a	n/a
27	ESR1	chr3:112887257-112887549	ECC-1	luminal epithelium:	n/a	n/a
28	ESR1	chr3:112885943-112886461	ECC-1	luminal epithelium:	n/a	n/a
29	ESR1	chr3:112887179-112887637	ECC-1	luminal epithelium:	n/a	n/a
30	ESR1	chr3:112887107-112887655	ECC-1	luminal epithelium:	n/a	n/a
31	FOS	chr3:112889932-112890124	MCF10A-Er-Src	breast:	n/a	n/a
32	FOXP2	chr3:112886002-112886399	SK-N-MC	brain:	n/a	n/a
33	GATA2	chr3:112893122-112893422	SH-SY5Y	brain:	n/a	n/a
34	GATA2	chr3:112885243-112887450	SH-SY5Y	brain:	n/a	chr3:112887115-112887122 chr3:112887115-112887122 chr3:112887115-112887122
35	GATA3	chr3:112891436-112891607	SH-SY5Y	brain:	n/a	n/a
36	GATA3	chr3:112885290-112886647	SK-N-SH	brain:	n/a	n/a
37	GATA3	chr3:112885454-112886606	SK-N-SH	brain:	n/a	n/a
38	GATA3	chr3:112893062-112893338	SH-SY5Y	brain:	n/a	n/a
39	GATA3	chr3:112885725-112886029	T-47D	breast:	n/a	n/a
40	GATA3	chr3:112885491-112887201	SH-SY5Y	brain:	n/a	chr3:112887115-112887122 chr3:112887115-112887122 chr3:112887115-112887122
41	JUN	chr3:112880122-112880128	H1-hESC	embryonic stem cell:	n/a	n/a
42	KAP1	chr3:112885025-112887729	HEK293	kidney:	n/a	chr3:112885895-112885903
43	KAP1	chr3:112885284-112886567	U2OS	brain:	n/a	chr3:112885895-112885903
44	KAP1	chr3:112886783-112887704	U2OS	brain:	n/a	n/a
45	MAFK	chr3:112880445-112880769	HepG2	liver:	n/a	chr3:112880604-112880621
46	MAFK	chr3:112880494-112880745	HepG2	liver:	n/a	chr3:112880604-112880621
47	MAX	chr3:112885475-112886311	SK-N-SH	brain:	n/a	n/a
48	NFIC	chr3:112885496-112886505	SK-N-SH	brain:	n/a	chr3:112886171-112886188
49	NFIC	chr3:112885348-112886566	ECC-1	luminal epithelium:	n/a	chr3:112886171-112886188
50	NFIC	chr3:112885430-112886518	ECC-1	luminal epithelium:	n/a	chr3:112886171-112886188

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:112885856-112885906	Jurkat	blood:	n/a
2	chr3:112885856-112885906	PFSK-1	brain:	n/a
3	chr3:112885856-112885906	ProgFib	skin:	n/a
4	chr3:112885856-112885906	HCF	heart:	n/a
5	chr3:112885856-112885906	LNCaP	prostate:	n/a
6	chr3:112885856-112885906	AG04449	skin:	fetal
7	chr3:112885856-112885906	HepG2	liver:	n/a
8	chr3:112885856-112885906	RPTEC	kidney:	n/a
9	chr3:112885856-112885906	U87	brain:	n/a
10	chr3:112885856-112885906	AG10803	skin:	n/a
11	chr3:112885856-112885906	HRE	kidney:	n/a
12	chr3:112885856-112885906	H1-hESC	embryonic stem cell:	embryo
13	chr3:112885856-112885906	HCPEpiC	choroid plexus:	n/a
14	chr3:112885856-112885906	ovcar-3	ovarian:	n/a
15	chr3:112885856-112885906	HPAEpiC	pulmonary alveolar:	n/a
16	chr3:112885856-112885906	HCT-116	colon:	n/a
17	chr3:112885856-112885906	HCM	heart:	n/a
18	chr3:112885856-112885906	AoSMC	blood vessel:	n/a
19	chr3:112885856-112885906	IMR90	lung:	fetal
20	chr3:112885856-112885906	HNPCEpiC	eye:	n/a
21	chr3:112885856-112885906	HRPEpiC	eye:	n/a
22	chr3:112885856-112885906	HAEpiC	amniotic membrane:	n/a
23	chr3:112885856-112885906	Hepatocyte	liver:	n/a
24	chr3:112885856-112885906	AG09309	skin:	n/a
25	chr3:112885856-112885906	SKMC	muscle:	n/a
26	chr3:112885856-112885906	GM19239	blood:	n/a
27	chr3:112885856-112885906	HUVEC	blood vessel:	n/a
28	chr3:112885856-112885906	HRCEpiC	kidney:	n/a
29	chr3:112885856-112885906	MCF10A-Er-Src	breast:	n/a
30	chr3:112885856-112885906	NT2-D1	testis:	n/a
31	chr3:112885856-112885906	BJ	skin:	n/a
32	chr3:112885856-112885906	SK-N-MC	brain:	n/a
33	chr3:112885856-112885906	HMEC	breast:	n/a
34	chr3:112885856-112885906	BE2_C	brain:	n/a
35	chr3:112885856-112885906	HIPEpiC	eye:	n/a
36	chr3:112885856-112885906	SAEC	small airway:	n/a
37	chr3:112885856-112885906	SK-N-SH	brain:	n/a
38	chr3:112885856-112885906	PANC-1	pancreas:	n/a
39	chr3:112885856-112885906	GM12878	blood:	n/a
40	chr3:112885856-112885906	HL-60	blood:	n/a
41	chr3:112885856-112885906	NB4	blood:	n/a
42	chr3:112885856-112885906	SK-N-SH_RA	brain:	n/a
43	chr3:112885856-112885906	CMK	blood:	n/a
44	chr3:112885856-112885906	HEK293	kidney:	embryo
45	chr3:112885856-112885906	HEEpiC	esophagus:	n/a
46	chr3:112885856-112885906	AG09319	gingival:	n/a
47	chr3:112885856-112885906	A549	lung:	n/a
48	chr3:112885856-112885906	NHDF-neo	bronchial:	n/a
49	chr3:112885856-112885906	T-47D	breast:	n/a
50	chr3:112885856-112885906	Caco-2	colon:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDR52-1	chr3:112883974-112884053	XLOC_003220
2	lnc-WDR52-1	chr3:112886448-112886666	XLOC_003220
3	lnc-GTPBP8-1	chr3:112883900-112884294	NONHSAT091221
4	lnc-GTPBP8-1	chr3:112880343-112880866	NONHSAT091221
5	lnc-GTPBP8-1	chr3:112883901-112884294	XLOC_002760
6	lnc-GTPBP8-1	chr3:112880781-112880867	XLOC_002760
7	lnc-GTPBP8-1	chr3:112880344-112880866	XLOC_002760
8	lnc-GTPBP8-1	chr3:112880781-112880866	ENSG00000240057.1
9	lnc-GTPBP8-1	chr3:112880781-112880866	XLOC_002760

No data

Variant related genes	Relation type
ENSG00000243795	TF binding region
ENSG00000243795	CpG island
KDM3A	miRNA target sites

Extended variants
information (count: 586 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:586 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs10934223	chr3:112878536-112878537	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs10934224	chr3:112878571-112878572	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs573124296	chr3:112878599-112878600	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs540488848	chr3:112878645-112878646	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs564255515	chr3:112878656-112878657	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs190266338	chr3:112878662-112878663	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs115450710	chr3:112878679-112878680	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs537004077	chr3:112878721-112878722	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs57075327	chr3:112878730-112878731	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs562930321	chr3:112878847-112878848	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs181468098	chr3:112878851-112878852	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs186947576	chr3:112878870-112878871	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs147337412	chr3:112878929-112878930	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs62264172	chr3:112878961-112878962	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs552453361	chr3:112879003-112879004	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs1997389	chr3:112879015-112879016	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs527882405	chr3:112879024-112879025	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs34162902	chr3:112879064-112879065	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs564736961	chr3:112879084-112879085	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs369499294	chr3:112879132-112879133	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs571073049	chr3:112879142-112879143	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs534958940	chr3:112879243-112879244	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs566481982	chr3:112879247-112879248	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs532102639	chr3:112879283-112879284	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs189745424	chr3:112879284-112879285	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs138950722	chr3:112879361-112879362	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs201375538	chr3:112879401-112879402	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs552892511	chr3:112879442-112879443	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs536341774	chr3:112879445-112879446	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs554710863	chr3:112879458-112879459	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs566634004	chr3:112879462-112879463	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs533994931	chr3:112879514-112879515	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs11915640	chr3:112879515-112879516	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs149338641	chr3:112879534-112879535	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs57521234	chr3:112879615-112879616	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs13086237	chr3:112879711-112879712	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs530840522	chr3:112879714-112879715	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs541873698	chr3:112879716-112879717	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs560221047	chr3:112879762-112879763	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs148525426	chr3:112879784-112879785	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs374573061	chr3:112879809-112879810	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs546006695	chr3:112879814-112879815	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs181210516	chr3:112879816-112879817	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs185429355	chr3:112879875-112879876	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs550488883	chr3:112879876-112879877	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs189745852	chr3:112879894-112879895	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs145388824	chr3:112879915-112879916	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs58885804	chr3:112879984-112879985	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs572842226	chr3:112879986-112879987	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs376275974	chr3:112880008-112880009	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:61)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Neurodevelopmental disorder	22521361	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	16608533	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Developmental delay	22180640	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Multiple myeloma	17550852	CNVD
small cell lung cancer	20016488	CNVD
Basal cell lymphoma	21115979	CNVD
Attention deficit hyperactivity disorder	22180640	CNVD
Breast cancer	17142309	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Ovarian cancer	22174824	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:240 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112871000-112881400	Weak transcription	Fetal Lung	lung
2	chr3:112875600-112880200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:112876800-112884000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:112876800-112885000	Weak transcription	Fetal Kidney	kidney
5	chr3:112877000-112881800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:112878400-112884000	Weak transcription	Fetal Stomach	stomach
7	chr3:112880000-112881200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:112880200-112880800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:112880200-112881200	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr3:112880800-112885200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:112881000-112882200	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:112881200-112884000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:112881200-112884000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:112881400-112882400	Enhancers	Fetal Lung	lung
15	chr3:112881800-112882400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:112882200-112882400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:112882200-112882400	Enhancers	Fetal Muscle Leg	muscle
18	chr3:112882400-112883800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:112882400-112883800	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:112882400-112884400	Weak transcription	Fetal Lung	lung
21	chr3:112883800-112884200	Enhancers	H1 Cell Line	embryonic stem cell
22	chr3:112883800-112884200	Enhancers	Fetal Muscle Trunk	muscle
23	chr3:112883800-112886600	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr3:112883800-112886600	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr3:112883800-112887800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:112883800-112889400	Enhancers	Fetal Muscle Leg	muscle
27	chr3:112884000-112884200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:112884000-112885600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:112884000-112885600	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr3:112884000-112886600	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr3:112884000-112887000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:112884000-112887400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:112884000-112889200	Enhancers	Fetal Stomach	stomach
34	chr3:112884000-112889600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:112884000-112889600	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr3:112884200-112884400	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:112884200-112885200	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr3:112884200-112885400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr3:112884200-112887200	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr3:112884200-112888800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:112884400-112885200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:112884400-112885600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:112884400-112885600	Enhancers	Colon Smooth Muscle	Colon
44	chr3:112884400-112886400	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr3:112884400-112887800	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr3:112884400-112889400	Enhancers	Fetal Lung	lung
47	chr3:112884800-112885400	Enhancers	Fetal Thymus	thymus
48	chr3:112884800-112885600	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr3:112884800-112885600	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr3:112884800-112886400	Enhancers	Placenta	Placenta

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