Variant report

Variant	esv1815803
Chromosome Location	chr2:48848295-48870365
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	chr2:48850023-48850151	K562	blood:	n/a	n/a
2	CCNT2	chr2:48860293-48860625	K562	blood:	n/a	n/a
3	CEBPB	chr2:48850005-48850195	K562	blood:	n/a	n/a
4	CEBPB	chr2:48862820-48862911	IMR90	lung:	n/a	n/a
5	CEBPD	chr2:48860331-48860701	K562	blood:	n/a	n/a
6	CEBPD	chr2:48860224-48860663	K562	blood:	n/a	n/a
7	CHD1	chr2:48861003-48861083	GM12878	blood:	n/a	n/a
8	CTCF	chr2:48850060-48850210	K562	blood:	n/a	n/a
9	CTCF	chr2:48849922-48850203	IMR90	lung:	n/a	chr2:48850043-48850064
10	CTCF	chr2:48849958-48850141	Hela-S3	cervix:	n/a	chr2:48850043-48850064
11	CTCF	chr2:48850020-48850170	HepG2	liver:	n/a	chr2:48850043-48850064
12	CTCF	chr2:48850000-48850150	HMF	breast:	n/a	chr2:48850043-48850064
13	CTCF	chr2:48849940-48850090	HEK293	kidney:	n/a	chr2:48850043-48850064
14	CTCF	chr2:48849960-48850110	AG09309	skin:	n/a	chr2:48850043-48850064
15	CTCF	chr2:48850020-48850170	MCF-7	breast:	n/a	chr2:48850043-48850064
16	CTCF	chr2:48861940-48862090	GM12872	blood:	n/a	n/a
17	CTCF	chr2:48849980-48850130	AG10803	skin:	n/a	chr2:48850043-48850064
18	CTCF	chr2:48849878-48850195	GM12878	blood:	n/a	chr2:48850043-48850064
19	CTCF	chr2:48862000-48862150	HepG2	liver:	n/a	n/a
20	CTCF	chr2:48850000-48850150	NHDF-neo	bronchial:	n/a	chr2:48850043-48850064
21	CTCF	chr2:48862000-48862150	GM12864	blood:	n/a	n/a
22	CTCF	chr2:48849810-48850318	A549	lung:	n/a	chr2:48850043-48850064
23	CTCF	chr2:48863091-48863146	GM13976	blood:	n/a	n/a
24	CTCF	chr2:48849911-48850219	MCF-7	breast:	n/a	chr2:48850043-48850064
25	CTCF	chr2:48861940-48862090	GM12873	blood:	n/a	n/a
26	CTCF	chr2:48849980-48850130	GM12865	blood:	n/a	chr2:48850043-48850064
27	CTCF	chr2:48849971-48850115	LNCaP	prostate:	n/a	chr2:48850043-48850064
28	CTCF	chr2:48849953-48850070	MCF-7	breast:	n/a	chr2:48850043-48850064
29	CTCF	chr2:48849862-48850247	K562	blood:	n/a	chr2:48850043-48850064
30	CTCF	chr2:48849940-48850090	AG10803	skin:	n/a	chr2:48850043-48850064
31	CTCF	chr2:48849900-48850050	AoAF	blood vessel:	n/a	n/a
32	CTCF	chr2:48849920-48850070	AG09319	gingival:	n/a	chr2:48850043-48850064
33	CTCF	chr2:48849965-48850148	Medullo	brain:	n/a	chr2:48850043-48850064
34	CTCF	chr2:48849990-48850128	LNCaP	prostate:	n/a	chr2:48850043-48850064
35	CTCF	chr2:48849940-48850090	GM06990	blood:	n/a	chr2:48850043-48850064
36	CTCF	chr2:48862020-48862170	GM12870	blood:	n/a	n/a
37	CTCF	chr2:48849980-48850130	Hela-S3	cervix:	n/a	chr2:48850043-48850064
38	CTCF	chr2:48849960-48850110	K562	blood:	n/a	chr2:48850043-48850064
39	CTCF	chr2:48849980-48850130	SK-N-SH_RA	brain:	n/a	chr2:48850043-48850064
40	CTCF	chr2:48849980-48850130	Caco-2	colon:	n/a	chr2:48850043-48850064
41	CTCF	chr2:48850000-48850150	MCF-7	breast:	n/a	chr2:48850043-48850064
42	CTCF	chr2:48849980-48850130	AG09319	gingival:	n/a	chr2:48850043-48850064
43	CTCF	chr2:48849966-48850136	K562	blood:	n/a	chr2:48850043-48850064
44	CTCF	chr2:48849980-48850130	HCFaa	heart:	n/a	chr2:48850043-48850064
45	EGR1	chr2:48860430-48860684	K562	blood:	n/a	n/a
46	EGR1	chr2:48860392-48860681	K562	blood:	n/a	n/a
47	EP300	chr2:48860367-48860629	K562	blood:	n/a	n/a
48	GABPA	chr2:48860392-48860634	K562	blood:	n/a	n/a
49	GABPA	chr2:48860356-48860548	K562	blood:	n/a	n/a
50	GATA2	chr2:48860299-48860659	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:48848421-48848471	HEEpiC	esophagus:	n/a
2	chr2:48848421-48848471	ProgFib	skin:	n/a
3	chr2:48848421-48848471	HPAEpiC	pulmonary alveolar:	n/a
4	chr2:48848421-48848471	H1-hESC	embryonic stem cell:	embryo
5	chr2:48848421-48848471	HIPEpiC	eye:	n/a
6	chr2:48848421-48848471	GM12891	blood:	n/a
7	chr2:48848421-48848471	BJ	skin:	n/a
8	chr2:48848421-48848471	HMEC	breast:	n/a
9	chr2:48848421-48848471	HCT-116	colon:	n/a
10	chr2:48848421-48848471	IMR90	lung:	fetal
11	chr2:48848421-48848471	GM06990	blood:	n/a
12	chr2:48848421-48848471	AG04449	skin:	fetal
13	chr2:48848421-48848471	NHDF-neo	bronchial:	n/a
14	chr2:48848421-48848471	SK-N-SH_RA	brain:	n/a
15	chr2:48848421-48848471	AG04450	lung:	fetal
16	chr2:48848421-48848471	HepG2	liver:	n/a
17	chr2:48848421-48848471	AG09319	gingival:	n/a
18	chr2:48848421-48848471	BE2_C	brain:	n/a
19	chr2:48848421-48848471	MCF10A-Er-Src	breast:	n/a
20	chr2:48848421-48848471	HAEpiC	amniotic membrane:	n/a
21	chr2:48848421-48848471	Jurkat	blood:	n/a
22	chr2:48848421-48848471	HCM	heart:	n/a
23	chr2:48848421-48848471	SK-N-SH	brain:	n/a
24	chr2:48848421-48848471	PFSK-1	brain:	n/a
25	chr2:48848421-48848471	U87	brain:	n/a
26	chr2:48848421-48848471	NH-A	brain:	n/a
27	chr2:48848421-48848471	PANC-1	pancreas:	n/a
28	chr2:48848421-48848471	Hepatocyte	liver:	n/a
29	chr2:48848421-48848471	NT2-D1	testis:	n/a
30	chr2:48848421-48848471	Hela-S3	cervix:	n/a
31	chr2:48848421-48848471	SKMC	muscle:	n/a
32	chr2:48848421-48848471	SK-N-MC	brain:	n/a
33	chr2:48848421-48848471	HEK293	kidney:	embryo
34	chr2:48848421-48848471	T-47D	breast:	n/a
35	chr2:48848421-48848471	Caco-2	colon:	n/a
36	chr2:48848421-48848471	SAEC	small airway:	n/a
37	chr2:48848421-48848471	A549	lung:	n/a
38	chr2:48848421-48848471	GM12892	blood:	n/a
39	chr2:48848421-48848471	AoSMC	blood vessel:	n/a
40	chr2:48848421-48848471	HRE	kidney:	n/a
41	chr2:48848421-48848471	AG09309	skin:	n/a
42	chr2:48848421-48848471	K562	blood:	n/a
43	chr2:48848421-48848471	RPTEC	kidney:	n/a
44	chr2:48848421-48848471	GM12878	blood:	n/a
45	chr2:48848421-48848471	LNCaP	prostate:	n/a
46	chr2:48848421-48848471	HNPCEpiC	eye:	n/a
47	chr2:48848421-48848471	NB4	blood:	n/a
48	chr2:48848421-48848471	CMK	blood:	n/a
49	chr2:48848421-48848471	HCPEpiC	choroid plexus:	n/a
50	chr2:48848421-48848471	MCF-7	breast:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48837425..48839347-chr2:48846973..48850503,3	K562	blood:
2	chr2:48845784..48847693-chr2:48848992..48850627,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LHCGR-1	chr2:48859428-48860260	NONHSAT070627
2	lnc-LHCGR-1	chr2:48859995-48860492	NONHSAT070628

Variant related genes	Relation type
TPT1P11	TF binding region
TPT1P11	CpG island

Extended variants
information (count: 983 )
Associated
traits (count: 86 )

Variant overlapped rSNPs/rCNVs (count:983 , 50 per page) page: 1 2 3 4 5 6 7 ... 20

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs201450137	chr2:48848295-48848296	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs62137485	chr2:48848298-48848299	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs201134669	chr2:48848329-48848330	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs78467696	chr2:48848353-48848354	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs138366256	chr2:48848375-48848376	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs369180876	chr2:48848376-48848377	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs565482782	chr2:48848387-48848388	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs375824947	chr2:48848394-48848395	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs202215091	chr2:48848398-48848399	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs150508709	chr2:48848454-48848455	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs377562020	chr2:48848468-48848469	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs369527689	chr2:48848476-48848477	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs560074256	chr2:48848510-48848511	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs17037472	chr2:48848515-48848516	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs548281031	chr2:48848516-48848517	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs570285050	chr2:48848533-48848534	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs17037474	chr2:48848548-48848549	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs373817134	chr2:48848578-48848579	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs184321887	chr2:48848582-48848583	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs376791149	chr2:48848587-48848588	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs189654284	chr2:48848595-48848596	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs141591768	chr2:48848620-48848621	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs2103113	chr2:48848640-48848641	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs552860811	chr2:48848685-48848686	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs111744020	chr2:48848687-48848688	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs553679871	chr2:48848689-48848690	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs376919033	chr2:48848710-48848711	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs146213371	chr2:48848717-48848718	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs139273425	chr2:48848724-48848725	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs181043363	chr2:48848729-48848730	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs545585064	chr2:48848736-48848737	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs17037477	chr2:48848796-48848797	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs564940179	chr2:48848810-48848811	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs185517077	chr2:48848820-48848821	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs571056957	chr2:48848825-48848826	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs112627496	chr2:48848834-48848835	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs369242988	chr2:48848859-48848860	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs560128145	chr2:48848885-48848886	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs149513540	chr2:48848900-48848901	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs377626143	chr2:48848954-48848955	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs548816206	chr2:48848975-48848976	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs79480575	chr2:48849025-48849026	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs553542604	chr2:48849053-48849054	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs1996969	chr2:48849066-48849067	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
45	rs17398030	chr2:48849124-48849125	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
46	rs118127567	chr2:48849153-48849154	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs144071203	chr2:48849216-48849217	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs536161688	chr2:48849220-48849221	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs554820391	chr2:48849233-48849234	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs557345723	chr2:48849286-48849287	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:86)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Bladder cancer	21909424	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Lung cancer	17297452	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Breast cancer	21364760	CNVD
Schizophrenia	20433910	CNVD
Autism	21701786	CNVD
Attention deficit hyperactivity disorder	21324949	CNVD
Austim spectrum disorder	21302340	CNVD
Schizophrenia	20587603	CNVD
Schizophrenia	20553308	CNVD
Autism	22241247	CNVD
Myelofibrosis	22110671	CNVD
Lung adenocarcinoma	17086460	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Acute lymphoblastic leukemia	18768390	CNVD
Mental retardation	19521722	CNVD
Schizophrenia	18990708	CNVD
Schizophrenia	18940311	CNVD
Schizophrenia	19348701	CNVD
Schizophrenia	18945720	CNVD
Schizophrenia	19571808	CNVD
Prostate cancer	16573809	CNVD
Neuroticism	17667963	CNVD
Schizophrenia	19443537	CNVD
Schizophrenia	19546859	CNVD
Autism	17322880	CNVD
Lung cancer	17086460	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	22522925	CNVD
T-cell lymphomas	22341440	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48831000-48859600	Weak transcription	Ovary	ovary
2	chr2:48836600-48862000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:48847000-48853000	Weak transcription	Colon Smooth Muscle	Colon
4	chr2:48853000-48853400	ZNF genes & repeats	Colon Smooth Muscle	Colon
5	chr2:48853000-48854000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
6	chr2:48853400-48853800	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:48854000-48873600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:48859600-48860000	ZNF genes & repeats	Ovary	ovary
9	chr2:48860000-48862000	Weak transcription	Ovary	ovary
10	chr2:48860200-48860600	Enhancers	K562	blood
11	chr2:48860400-48860600	Enhancers	Lung	lung
12	chr2:48860400-48860600	ZNF genes & repeats	Right Atrium	heart
13	chr2:48860600-48862000	Weak transcription	Lung	lung
14	chr2:48860600-48863000	Weak transcription	Right Atrium	heart
15	chr2:48862000-48862200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:48862000-48862800	ZNF genes & repeats	Lung	lung
17	chr2:48862000-48863000	ZNF genes & repeats	Aorta	Aorta
18	chr2:48862000-48863000	Strong transcription	Stomach Smooth Muscle	stomach
19	chr2:48862000-48863200	Strong transcription	Ovary	ovary
20	chr2:48862200-48862600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:48862600-48863000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:48862600-48863400	Enhancers	Placenta Amnion	Placenta Amnion
23	chr2:48863000-48898200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:48863000-48919600	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:48863200-48873600	Weak transcription	Ovary	ovary
26	chr2:48868600-48869000	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr2:48869800-48915400	Weak transcription	Adipose Nuclei	Adipose

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