Variant report

Variant	nsv1000388
Chromosome Location	chr1:78638946-78665285
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	BATF	chr1:78650163-78650703	GM12878	blood:	n/a	n/a
2	BCL11A	chr1:78650331-78650726	GM12878	blood:	n/a	n/a
3	CEBPB	chr1:78646033-78646292	A549	lung:	n/a	chr1:78646171-78646182
4	CEBPB	chr1:78646185-78646189	H1-hESC	embryonic stem cell:	n/a	n/a
5	CEBPB	chr1:78646069-78646269	K562	blood:	n/a	chr1:78646171-78646182
6	CEBPB	chr1:78646000-78646304	HepG2	liver:	n/a	chr1:78646171-78646182
7	CEBPB	chr1:78646047-78646360	IMR90	lung:	n/a	chr1:78646171-78646182
8	CTCF	chr1:78643020-78643170	HMEC	breast:	n/a	n/a
9	EBF1	chr1:78650281-78650343	GM12878	blood:	n/a	n/a
10	EP300	chr1:78642217-78642454	SK-N-SH_RA	brain:	n/a	n/a
11	FOS	chr1:78642111-78642460	MCF10A-Er-Src	breast:	n/a	chr1:78642271-78642279
12	FOS	chr1:78642105-78642505	MCF10A-Er-Src	breast:	n/a	chr1:78642271-78642279
13	FOS	chr1:78642120-78642478	MCF10A-Er-Src	breast:	n/a	chr1:78642271-78642279
14	FOS	chr1:78642145-78642442	MCF10A-Er-Src	breast:	n/a	chr1:78642271-78642279
15	GATA3	chr1:78644737-78645281	SK-N-SH	brain:	n/a	n/a
16	GATA3	chr1:78661112-78661618	SK-N-SH	brain:	n/a	n/a
17	GATA3	chr1:78661078-78661665	SK-N-SH	brain:	n/a	n/a
18	GATA3	chr1:78641934-78642625	SK-N-SH	brain:	n/a	n/a
19	GTF2F1	chr1:78642305-78642351	Hela-S3	cervix:	n/a	n/a
20	JUND	chr1:78642009-78642614	SK-N-SH	brain:	n/a	chr1:78642271-78642279
21	MAFK	chr1:78639036-78639175	HepG2	liver:	n/a	n/a
22	MYC	chr1:78642123-78642524	MCF10A-Er-Src	breast:	n/a	chr1:78642270-78642279
23	MYC	chr1:78642140-78642434	MCF10A-Er-Src	breast:	n/a	chr1:78642270-78642279
24	MYC	chr1:78644588-78644728	H1-hESC	embryonic stem cell:	n/a	n/a
25	NFIC	chr1:78642186-78642586	ECC-1	luminal epithelium:	n/a	n/a
26	NFIC	chr1:78641981-78642714	SK-N-SH	brain:	n/a	n/a
27	NFIC	chr1:78661140-78661641	SK-N-SH	brain:	n/a	n/a
28	NFIC	chr1:78642063-78642553	ECC-1	luminal epithelium:	n/a	n/a
29	NFYB	chr1:78643784-78643966	GM12878	blood:	n/a	n/a
30	PBX3	chr1:78661173-78661723	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr1:78644470-78644920	HepG2	liver:	n/a	n/a
32	POLR2A	chr1:78647468-78647585	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:78642319-78642434	MCF10A-Er-Src	breast:	n/a	n/a
34	RAD21	chr1:78642161-78642502	SK-N-SH_RA	brain:	n/a	n/a
35	REST	chr1:78642157-78642443	SK-N-SH	brain:	n/a	n/a
36	RUNX3	chr1:78650353-78650606	GM12878	blood:	n/a	n/a
37	SRF	chr1:78642124-78642611	ECC-1	luminal epithelium:	n/a	n/a
38	SRF	chr1:78642229-78642531	ECC-1	luminal epithelium:	n/a	n/a
39	STAT3	chr1:78642305-78642527	MCF10A-Er-Src	breast:	n/a	n/a
40	STAT3	chr1:78642205-78642460	MCF10A-Er-Src	breast:	n/a	n/a
41	TCF12	chr1:78661124-78661772	SK-N-SH	brain:	n/a	n/a
42	TCF12	chr1:78661119-78661659	SK-N-SH	brain:	n/a	n/a
43	TCF12	chr1:78641983-78642700	SK-N-SH	brain:	n/a	n/a
44	USF2	chr1:78642261-78642369	Hela-S3	cervix:	n/a	n/a
45	USF2	chr1:78661707-78661721	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
RNFT1P2	TF binding region

Extended variants
information (count: 551 )
Associated
traits (count: 103 )

Variant overlapped rSNPs/rCNVs (count:551 , 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	rs4650471	chr1:78638977-78638978	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs576833181	chr1:78639007-78639008	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs544229967	chr1:78639012-78639013	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs562897549	chr1:78639052-78639053	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs141482658	chr1:78639057-78639058	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs530366889	chr1:78639085-78639086	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs374868506	chr1:78639086-78639087	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs548846750	chr1:78639123-78639124	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs181740062	chr1:78639181-78639182	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs150557581	chr1:78639209-78639210	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs689374	chr1:78639244-78639245	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs570522151	chr1:78639252-78639253	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs372438694	chr1:78639323-78639324	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs537851868	chr1:78639337-78639338	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs549561359	chr1:78639339-78639340	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs568041878	chr1:78639343-78639344	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs186279895	chr1:78639354-78639355	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs189615321	chr1:78639379-78639380	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs569175812	chr1:78639404-78639405	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs568252911	chr1:78639405-78639406	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs139577008	chr1:78639431-78639432	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs182261341	chr1:78639460-78639461	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs558626658	chr1:78639476-78639477	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs187719141	chr1:78639519-78639520	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs4650476	chr1:78639530-78639531	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs12403493	chr1:78639533-78639534	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs547250369	chr1:78639543-78639544	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs562213631	chr1:78639547-78639548	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs149737613	chr1:78639565-78639566	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs542180082	chr1:78639606-78639607	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs560733760	chr1:78639614-78639615	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs12410030	chr1:78639640-78639641	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs78775723	chr1:78639647-78639648	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs6694656	chr1:78639840-78639841	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs531349533	chr1:78639879-78639880	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs191342458	chr1:78639904-78639905	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs140115866	chr1:78639924-78639925	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs200460303	chr1:78639925-78639926	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs201298039	chr1:78639926-78639927	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs567994287	chr1:78640031-78640032	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs528844564	chr1:78640032-78640033	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs556195270	chr1:78640033-78640034	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs368489995	chr1:78640038-78640039	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs183219468	chr1:78640041-78640042	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs539342183	chr1:78640055-78640056	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs627549	chr1:78640109-78640110	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs569816694	chr1:78640118-78640119	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs537981996	chr1:78640130-78640131	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs556592747	chr1:78640131-78640132	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs1770306	chr1:78640222-78640223	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:103)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Colorectal cancer	16272173	CNVD
Wilms tumour	21544195	CNVD
Coronary Disease	20032323	CNVD
Prostate cancer	21965145	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Stargardt''s disease	17277736	CNVD
Neuroblastoma	17897457	CNVD
Uveal melanoma	21693616	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-syndromic sensorineural hearing loss	22290220	CNVD
Liposarcoma	21253554	CNVD
Breast cancer	21264507	CNVD
Acute myeloid leukemia	16864856	CNVD
Astrocytoma	17387387	CNVD
Cancer	21499728	CNVD
Glioblastoma multiforme	17387387	CNVD
Oligodendroglial tumors	17285580	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Neuroblastoma	17535989	CNVD
Pheochromocytoma	17535989	CNVD
Prostate cancer	16705090	CNVD
Astrocytoma	17934521	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Gastrointestinal stromal cancer	17535989	CNVD
Neuroblastoma	17533364	CNVD
Paraganglioma	17535989	CNVD
Pulmonary chondroma	17535989	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	22495311	CNVD
Non-small cell lung cancer	21385341	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Chordoma	21602918	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Melanoma	18172304	CNVD
Multiple myeloma	16461302	CNVD
Melanoma	17363583	CNVD
Cancer	21129771	CNVD
Autosomal dominant nocturnal frontal lobe epilepsy	18472482	CNVD
Hirschsprung''s Disease	21712996	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Thrombocytopenia-absent radius syndrome	21933853	CNVD
Psychiatric disorder	22848183	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Hepatocellular carcinoma	16750200	CNVD
Burkitt''s lymphoma	18698080	CNVD
Breast cancer	20409316	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Lung cancer	18438408	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17393978	CNVD
Cervical cancer	21062161	CNVD
Cancer	21183584	CNVD
Breast cancer	21785460	CNVD
Breast cancer	21364760	CNVD
Rett syndrome	21593744	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	16608533	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	17133270	CNVD
Type 2 diabetes	21956041	CNVD
Uveal melanoma	20484589	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Ewing''s sarcoma	17952124	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Poland''s syndrome	22110015	CNVD
Glioblastoma multiforme	22286061	CNVD
Glioblastoma multiforme	21922591	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Cancer	22429812	CNVD
Effusion lymphoma	18079361	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Colorectal cancer	16774939	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78625200-78644400	Weak transcription	Pancreas	Pancrea
2	chr1:78635000-78646200	Weak transcription	Fetal Intestine Small	intestine
3	chr1:78637200-78639400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr1:78638400-78641800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:78638400-78641800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:78638600-78639000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:78638600-78641600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:78638600-78641600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:78638600-78641800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:78638600-78641800	Weak transcription	HSMM	muscle
11	chr1:78638600-78641800	Weak transcription	NHDF-Ad	bronchial
12	chr1:78638600-78641800	Weak transcription	NHEK	skin
13	chr1:78638600-78641800	Weak transcription	Osteobl	bone
14	chr1:78638600-78642000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:78638800-78641800	Weak transcription	HMEC	breast
16	chr1:78638800-78642000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:78638800-78642000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:78639000-78641600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:78641600-78642800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:78641600-78642800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:78641600-78643400	Enhancers	Fetal Muscle Leg	muscle
22	chr1:78641600-78643800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:78641800-78642200	Enhancers	HSMM	muscle
24	chr1:78641800-78642400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:78641800-78642600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:78641800-78642600	Enhancers	HMEC	breast
27	chr1:78641800-78642600	Enhancers	NHEK	skin
28	chr1:78641800-78642800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:78641800-78643200	Enhancers	Osteobl	bone
30	chr1:78641800-78643800	Enhancers	NHDF-Ad	bronchial
31	chr1:78641800-78645200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:78642000-78642400	Enhancers	Brain Germinal Matrix	brain
33	chr1:78642000-78642600	Enhancers	Muscle Satellite Cultured Cells	--
34	chr1:78642000-78642600	Enhancers	Stomach Smooth Muscle	stomach
35	chr1:78642000-78643200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:78642000-78643400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:78642000-78643800	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr1:78642200-78642600	Enhancers	HSMMtube	muscle
39	chr1:78643000-78643200	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr1:78643000-78643400	Enhancers	Fetal Thymus	thymus
41	chr1:78643200-78644400	Weak transcription	Osteobl	bone
42	chr1:78644400-78644800	Enhancers	Pancreas	Pancrea
43	chr1:78644800-78645000	Enhancers	Osteobl	bone
44	chr1:78656200-78656600	ZNF genes & repeats	Liver	Liver
45	chr1:78656600-78668800	Weak transcription	Liver	Liver
46	chr1:78657600-78667200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr1:78657600-78669600	Weak transcription	Pancreas	Pancrea
48	chr1:78658800-78660200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:78659200-78659400	ZNF genes & repeats	Fetal Intestine Small	intestine
50	chr1:78659400-78668000	Weak transcription	Fetal Intestine Small	intestine

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