Variant report

Variant	nsv1003000
Chromosome Location	chr4:78188691-78255427
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	BRCA1	chr4:78230084-78230356	Hela-S3	cervix:	n/a	n/a
2	CBX3	chr4:78253824-78254202	K562	blood:	n/a	n/a
3	CBX3	chr4:78253746-78254319	HCT-116	colon:	n/a	n/a
4	CBX3	chr4:78253883-78254139	K562	blood:	n/a	n/a
5	CEBPB	chr4:78215423-78215638	IMR90	lung:	n/a	chr4:78215544-78215555
6	CEBPB	chr4:78215392-78215580	K562	blood:	n/a	chr4:78215544-78215555
7	CEBPB	chr4:78226915-78227276	MCF-7	breast:	n/a	chr4:78227117-78227130 chr4:78227117-78227128 chr4:78227118-78227129 chr4:78227117-78227130
8	CEBPB	chr4:78226971-78227260	K562	blood:	n/a	chr4:78227117-78227130 chr4:78227117-78227128 chr4:78227118-78227129 chr4:78227117-78227130
9	CEBPB	chr4:78215400-78215689	HepG2	liver:	n/a	chr4:78215544-78215555
10	CEBPB	chr4:78226987-78227290	HepG2	liver:	n/a	chr4:78227117-78227130 chr4:78227117-78227128 chr4:78227118-78227129 chr4:78227117-78227130
11	CEBPB	chr4:78227010-78227248	Hela-S3	cervix:	n/a	chr4:78227117-78227130 chr4:78227117-78227128 chr4:78227118-78227129 chr4:78227117-78227130
12	CHD2	chr4:78254095-78254505	H1-hESC	embryonic stem cell:	n/a	n/a
13	CHD2	chr4:78230108-78230195	HepG2	liver:	n/a	n/a
14	CTCF	chr4:78198600-78198750	GM12873	blood:	n/a	chr4:78198641-78198650
15	CTCF	chr4:78230160-78230310	HUVEC	blood vessel:	n/a	n/a
16	CTCF	chr4:78230080-78230245	SK-N-SH_RA	brain:	n/a	n/a
17	CTCF	chr4:78227023-78227188	MCF-7	breast:	n/a	chr4:78227096-78227117 chr4:78227101-78227119 chr4:78227103-78227116
18	CTCF	chr4:78198540-78198690	BE2_C	brain:	n/a	chr4:78198641-78198650
19	CTCF	chr4:78230160-78230310	Caco-2	colon:	n/a	n/a
20	CTCF	chr4:78197240-78197390	NHEK	skin:	n/a	n/a
21	CTCF	chr4:78226982-78227193	Medullo	brain:	n/a	chr4:78227096-78227117 chr4:78227101-78227119 chr4:78227103-78227116
22	CTCF	chr4:78230120-78230270	BE2_C	brain:	n/a	n/a
23	CTCF	chr4:78197220-78197370	GM12873	blood:	n/a	n/a
24	CTCF	chr4:78230120-78230270	GM12865	blood:	n/a	n/a
25	CTCF	chr4:78230160-78230310	AG09309	skin:	n/a	n/a
26	CTCF	chr4:78230134-78230256	Kidney_OC	kidney:	n/a	n/a
27	CTCF	chr4:78230440-78230590	HMEC	breast:	n/a	n/a
28	CTCF	chr4:78227046-78227181	LNCaP	prostate:	n/a	chr4:78227096-78227117 chr4:78227101-78227119 chr4:78227103-78227116
29	CTCF	chr4:78227040-78227190	GM12871	blood:	n/a	chr4:78227096-78227117 chr4:78227101-78227119 chr4:78227103-78227116
30	CTCF	chr4:78230120-78230270	GM12870	blood:	n/a	n/a
31	CTCF	chr4:78227100-78227250	GM12864	blood:	n/a	chr4:78227101-78227119 chr4:78227103-78227116
32	CTCF	chr4:78227042-78227044	LNCaP	prostate:	n/a	n/a
33	CTCF	chr4:78230120-78230270	HPF	lung:	n/a	n/a
34	CTCF	chr4:78227020-78227170	MCF-7	breast:	n/a	chr4:78227096-78227117 chr4:78227101-78227119 chr4:78227103-78227116
35	CTCF	chr4:78197303-78197420	K562	blood:	n/a	n/a
36	CTCF	chr4:78230160-78230310	A549	lung:	n/a	n/a
37	CTCF	chr4:78230160-78230310	GM12875	blood:	n/a	n/a
38	CTCF	chr4:78230140-78230290	NHDF-neo	bronchial:	n/a	n/a
39	CTCF	chr4:78230200-78230350	HFF	foreskin:	n/a	n/a
40	CTCF	chr4:78227020-78227170	HEEpiC	esophagus:	n/a	chr4:78227096-78227117 chr4:78227101-78227119 chr4:78227103-78227116
41	CTCF	chr4:78227070-78227170	K562	blood:	n/a	chr4:78227096-78227117 chr4:78227101-78227119 chr4:78227103-78227116
42	CTCF	chr4:78227260-78227410	WI-38	lung:	n/a	n/a
43	CTCF	chr4:78230060-78230210	GM12866	blood:	n/a	n/a
44	CTCF	chr4:78230086-78230316	Hela-S3	cervix:	n/a	n/a
45	CTCF	chr4:78230160-78230310	HA-sp	spinal cord:	n/a	n/a
46	CTCF	chr4:78230120-78230270	AG09319	gingival:	n/a	n/a
47	CTCF	chr4:78197286-78197491	K562	blood:	n/a	n/a
48	CTCF	chr4:78230091-78230321	LNCaP	prostate:	n/a	n/a
49	CTCF	chr4:78230157-78230312	Fibrobl	skin:	n/a	n/a
50	CTCF	chr4:78230140-78230290	HEEpiC	esophagus:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:78174499..78176837-chr4:78205161..78207032,2	MCF-7	breast:
2	chr4:78230184..78230702-chr4:78278364..78278865,2	MCF-7	breast:
3	chr4:78161416..78162110-chr4:78226527..78227315,3	MCF-7	breast:
4	chr4:78161398..78162211-chr4:78229720..78230660,3	MCF-7	breast:
5	chr4:78161284..78162458-chr4:78229777..78230742,7	K562	blood:
6	chr4:78182930..78185790-chr4:78187841..78189605,2	K562	blood:
7	chr4:78161311..78162711-chr4:78226629..78227614,14	MCF-7	breast:
8	chr4:78229797..78230625-chr4:78279333..78280102,3	MCF-7	breast:
9	chr4:78162165..78163774-chr4:78227168..78228953,2	MCF-7	breast:
10	chr4:77973179..77974099-chr4:78229775..78230650,3	K562	blood:
11	chr4:78160754..78162321-chr4:78226906..78228617,2	MCF-7	breast:
12	chr4:78155252..78157365-chr4:78224145..78227144,3	MCF-7	breast:
13	chr4:78236163..78238480-chr4:78287943..78289669,2	K562	blood:
14	chr4:78161188..78162532-chr4:78229476..78230856,15	MCF-7	breast:
15	chr4:78158067..78160012-chr4:78227264..78228770,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCNI-5	chr4:78232550-78233264	NONHSAT097052

Variant related genes	Relation type
ENSG00000250006	TF binding region

Extended variants
information (count: 3410 )
Associated
traits (count: 75 )

Variant overlapped rSNPs/rCNVs (count:3410 , 50 per page) page: 1 2 3 4 5 6 7 ... 69

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs373279857	chr4:78188728-78188729	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs553121965	chr4:78188738-78188739	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs572850127	chr4:78188740-78188741	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs545026700	chr4:78188753-78188754	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs373563177	chr4:78188760-78188761	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs576451303	chr4:78188806-78188807	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs2059104	chr4:78188859-78188860	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
8	rs200220465	chr4:78188863-78188864	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs368745084	chr4:78188871-78188872	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs2059105	chr4:78188874-78188875	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
11	rs139464095	chr4:78188884-78188885	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs192296489	chr4:78188914-78188915	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs530119602	chr4:78188951-78188952	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs200745276	chr4:78188994-78188995	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs2059106	chr4:78189012-78189013	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
16	rs561772758	chr4:78189040-78189041	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs28445892	chr4:78189062-78189063	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs146551887	chr4:78189094-78189095	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs552196268	chr4:78189117-78189118	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs572192526	chr4:78189130-78189131	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs569450216	chr4:78189132-78189133	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs538560254	chr4:78189193-78189194	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs559334757	chr4:78189213-78189214	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs377287457	chr4:78189227-78189228	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs568606969	chr4:78189240-78189241	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs183267587	chr4:78189257-78189258	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs17394978	chr4:78189260-78189261	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs564347862	chr4:78189263-78189264	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs572984314	chr4:78189318-78189319	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs371257249	chr4:78189340-78189341	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs532568413	chr4:78189348-78189349	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs558569569	chr4:78189392-78189393	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs57527588	chr4:78189435-78189436	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs57123831	chr4:78189456-78189457	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs59155004	chr4:78189466-78189467	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs386676316	chr4:78189467-78189468	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs60506622	chr4:78189468-78189469	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs115810832	chr4:78189504-78189505	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs540038916	chr4:78189543-78189544	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs560170409	chr4:78189559-78189560	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs79290290	chr4:78189561-78189562	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs77937338	chr4:78189618-78189619	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs577308513	chr4:78189643-78189644	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs562936616	chr4:78189652-78189653	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs531626012	chr4:78189661-78189662	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs17002506	chr4:78189663-78189664	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs17395041	chr4:78189677-78189678	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs17399165	chr4:78189748-78189749	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs548050746	chr4:78189749-78189750	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs566568636	chr4:78189753-78189754	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:75)

Disease	PMID	Source
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Medulloblastoma	21979893	CNVD
Neuroblastoma	18923191	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21858162	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	17603634	CNVD
Glioblastoma multiforme	21922591	CNVD
Parkinson disease	21956041	CNVD
Mental retardation	20522426	CNVD
delayed speech	20522426	CNVD
growth disorder	20522426	CNVD
Hepatocellular carcinoma	16750200	CNVD
Myxofibrosarcoma	16751306	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Parkinson disease	18923514	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Breast cancer	16272173	CNVD
Colorectal cancer	19359472	CNVD
Malignant mesothelioma	18160781	CNVD
Medulloblastoma	18056178	CNVD
Multiple myeloma	17077331	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Oral squamous cell carcinoma	17134496	CNVD
4q-syndrome	17576883	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Muscular dystrophy	21149563	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Cervical cancer	21062161	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Lung cancer	19208797	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21785460	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Myelodysplastic syndrome	21251322	CNVD
Multiple myeloma	17550852	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Chronic lymphocytic leukemia	18922857	CNVD
Cancer	22429812	CNVD
Multiple myeloma	16616336	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	18414403	CNVD
Myelofibrosis	22110671	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Breast cancer	21364760	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78180000-78190200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:78186600-78190400	Weak transcription	HMEC	breast
3	chr4:78188600-78190600	Enhancers	Placenta	Placenta
4	chr4:78190200-78191000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:78190200-78191000	Bivalent Enhancer	HSMMtube	muscle
6	chr4:78190200-78191400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:78190400-78191000	Enhancers	HMEC	breast
8	chr4:78190400-78191600	Enhancers	Placenta Amnion	Placenta Amnion
9	chr4:78190600-78191000	Weak transcription	Placenta	Placenta
10	chr4:78191000-78193600	Enhancers	Placenta	Placenta
11	chr4:78191000-78200000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:78193600-78205400	Weak transcription	Placenta	Placenta
13	chr4:78199600-78201200	Enhancers	HMEC	breast
14	chr4:78200000-78200800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:78200000-78201000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:78200000-78201000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:78200000-78201000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:78203200-78203600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:78203400-78203800	Enhancers	Adipose Nuclei	Adipose
20	chr4:78205200-78205600	Enhancers	HSMMtube	muscle
21	chr4:78205200-78205800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:78205400-78205800	Enhancers	Placenta	Placenta
23	chr4:78205800-78211600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:78210400-78210600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr4:78210600-78221800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr4:78213200-78214600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr4:78214400-78214600	Enhancers	Placenta	Placenta
28	chr4:78214600-78214800	Enhancers	H9 Cell Line	embryonic stem cell
29	chr4:78214600-78215200	Weak transcription	Placenta	Placenta
30	chr4:78215200-78216000	Enhancers	Placenta	Placenta
31	chr4:78219000-78222200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr4:78219600-78219800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:78219600-78219800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
34	chr4:78219600-78219800	Enhancers	Primary hematopoietic stem cells	blood
35	chr4:78219600-78219800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr4:78219600-78219800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:78219800-78222400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:78221400-78221600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:78221400-78221800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr4:78221600-78222400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:78221600-78222800	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr4:78221800-78222200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr4:78221800-78222400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr4:78221800-78222800	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr4:78221800-78222800	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr4:78221800-78222800	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr4:78221800-78222800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:78221800-78222800	Enhancers	Stomach Mucosa	stomach
49	chr4:78222000-78222400	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr4:78222000-78222400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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