Variant report

Variant	nsv877611
Chromosome Location	chr3:145525989-145653627
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	chr3:145617078-145617323	GM12878	blood:	n/a	chr3:145617167-145617178
2	BATF	chr3:145617031-145617299	GM12878	blood:	n/a	chr3:145617167-145617178
3	BATF	chr3:145617922-145618098	GM12878	blood:	n/a	chr3:145617976-145617987
4	BATF	chr3:145617884-145618161	GM12878	blood:	n/a	chr3:145617976-145617987
5	BCL11A	chr3:145617839-145618177	GM12878	blood:	n/a	chr3:145617979-145617988 chr3:145617980-145617989
6	BCL11A	chr3:145617942-145618090	GM12878	blood:	n/a	chr3:145617979-145617988 chr3:145617980-145617989
7	BHLHE40	chr3:145616343-145617288	GM12878	blood:	n/a	n/a
8	BHLHE40	chr3:145617829-145618365	GM12878	blood:	n/a	n/a
9	BHLHE40	chr3:145535736-145536028	GM12878	blood:	n/a	n/a
10	BRCA1	chr3:145531712-145531727	Hela-S3	cervix:	n/a	n/a
11	BRCA1	chr3:145602167-145602271	Hela-S3	cervix:	n/a	n/a
12	CEBPB	chr3:145590953-145591270	Hela-S3	cervix:	n/a	chr3:145591064-145591075
13	CEBPB	chr3:145627344-145627617	Hela-S3	cervix:	n/a	chr3:145627469-145627480
14	CEBPB	chr3:145578466-145578687	A549	lung:	n/a	chr3:145578531-145578542
15	CEBPB	chr3:145575793-145576148	HepG2	liver:	n/a	chr3:145575984-145575995
16	CEBPB	chr3:145566972-145567248	Hela-S3	cervix:	n/a	n/a
17	CEBPB	chr3:145564493-145564795	HepG2	liver:	n/a	chr3:145564643-145564654
18	CEBPB	chr3:145578393-145578651	HepG2	liver:	n/a	chr3:145578531-145578542
19	CEBPB	chr3:145617147-145617472	A549	lung:	n/a	chr3:145617318-145617329
20	CEBPB	chr3:145590915-145591255	A549	lung:	n/a	chr3:145591064-145591075
21	CEBPB	chr3:145627381-145627633	A549	lung:	n/a	chr3:145627469-145627480
22	CEBPB	chr3:145566953-145567259	A549	lung:	n/a	n/a
23	CEBPB	chr3:145590926-145591356	IMR90	lung:	n/a	chr3:145591064-145591075
24	CEBPB	chr3:145627345-145627605	IMR90	lung:	n/a	chr3:145627469-145627480
25	CEBPB	chr3:145615179-145615388	Hela-S3	cervix:	n/a	chr3:145615286-145615297
26	CEBPB	chr3:145617170-145617502	HepG2	liver:	n/a	chr3:145617318-145617329
27	CEBPB	chr3:145643113-145643361	A549	lung:	n/a	chr3:145643198-145643209 chr3:145643269-145643282 chr3:145643200-145643211 chr3:145643216-145643227
28	CEBPB	chr3:145566939-145567262	IMR90	lung:	n/a	n/a
29	CEBPB	chr3:145525914-145526064	H1-hESC	embryonic stem cell:	n/a	chr3:145525953-145525966
30	CEBPB	chr3:145575808-145576126	Hela-S3	cervix:	n/a	chr3:145575984-145575995
31	CEBPB	chr3:145572327-145572667	Hela-S3	cervix:	n/a	chr3:145572530-145572543
32	CEBPB	chr3:145615201-145615448	IMR90	lung:	n/a	chr3:145615286-145615297
33	CEBPB	chr3:145533471-145533784	H1-hESC	embryonic stem cell:	n/a	n/a
34	CEBPB	chr3:145643100-145643364	HepG2	liver:	n/a	chr3:145643198-145643209 chr3:145643269-145643282 chr3:145643200-145643211 chr3:145643216-145643227
35	CEBPB	chr3:145566939-145567274	H1-hESC	embryonic stem cell:	n/a	n/a
36	CEBPB	chr3:145575849-145576013	HepG2	liver:	n/a	chr3:145575984-145575995
37	CEBPB	chr3:145575765-145576066	MCF-7	breast:	n/a	chr3:145575984-145575995
38	CEBPB	chr3:145525867-145526117	MCF-7	breast:	n/a	chr3:145525953-145525966
39	CEBPB	chr3:145616337-145617569	Hela-S3	cervix:	n/a	chr3:145617318-145617329
40	CEBPB	chr3:145566934-145567275	HepG2	liver:	n/a	n/a
41	CEBPB	chr3:145581045-145581109	H1-hESC	embryonic stem cell:	n/a	n/a
42	CEBPB	chr3:145627345-145627654	HepG2	liver:	n/a	chr3:145627469-145627480
43	CEBPB	chr3:145590904-145591245	K562	blood:	n/a	chr3:145591064-145591075
44	CEBPB	chr3:145564643-145564762	H1-hESC	embryonic stem cell:	n/a	chr3:145564643-145564654
45	CEBPB	chr3:145575803-145576121	A549	lung:	n/a	chr3:145575984-145575995
46	CEBPB	chr3:145590915-145591265	HepG2	liver:	n/a	chr3:145591064-145591075
47	CEBPB	chr3:145617031-145617489	IMR90	lung:	n/a	chr3:145617318-145617329
48	CEBPB	chr3:145615167-145615415	HepG2	liver:	n/a	chr3:145615286-145615297
49	CHD1	chr3:145618779-145618801	GM12878	blood:	n/a	n/a
50	CHD2	chr3:145617860-145618182	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:145621110..145623041-chr3:145624593..145626157,2	K562	blood:
2	chr3:145621110..145623041-chr3:145624593..145626157,2	K562	blood:
3	chr3:145515573..145518093-chr3:145523034..145526059,3	MCF-7	breast:
4	chr3:145558279..145560976-chr3:145566285..145567836,2	MCF-7	breast:
5	chr3:145604775..145606383-chr3:145616815..145618517,2	MCF-7	breast:
6	chr3:145604775..145606383-chr3:145616815..145618517,2	MCF-7	breast:
7	chr3:145558279..145560976-chr3:145566285..145567836,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLOD2-6	chr3:145542044-145542526	NONHSAT092540

Variant related genes	Relation type
RPL21P39	TF binding region
ENSG00000244358	TF binding region

Extended variants
information (count: 2630 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:2630 , 50 per page) page: 1 2 3 4 5 6 7 ... 53

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs7643638	chr3:145525989-145525990	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs76558124	chr3:145525990-145525991	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs13071000	chr3:145526021-145526022	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs13071418	chr3:145526022-145526023	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs553714767	chr3:145526027-145526028	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs533015338	chr3:145526051-145526052	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs200925741	chr3:145526079-145526080	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs200942433	chr3:145526081-145526082	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs189653718	chr3:145526095-145526096	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs116003457	chr3:145526122-145526123	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs530555878	chr3:145526160-145526161	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs6440388	chr3:145526164-145526165	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs6440389	chr3:145526178-145526179	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs371106117	chr3:145526202-145526203	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs529468476	chr3:145526223-145526224	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs547931256	chr3:145526231-145526232	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs142436174	chr3:145526246-145526247	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs540109915	chr3:145526325-145526326	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs558211146	chr3:145526326-145526327	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs570049870	chr3:145526332-145526333	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs575790814	chr3:145526345-145526346	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs150935452	chr3:145526346-145526347	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs555574544	chr3:145526373-145526374	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs140268461	chr3:145526410-145526411	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs534525172	chr3:145526424-145526425	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs182295743	chr3:145526468-145526469	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs577546667	chr3:145526473-145526474	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs371096416	chr3:145526485-145526486	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs6440390	chr3:145526526-145526527	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs574892783	chr3:145526545-145526546	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs542564027	chr3:145526568-145526569	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs560829859	chr3:145526578-145526579	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs535335924	chr3:145526594-145526595	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs4128173	chr3:145526611-145526612	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs547695117	chr3:145526641-145526642	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs559964880	chr3:145526650-145526651	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs370162689	chr3:145526655-145526656	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs533702640	chr3:145526678-145526679	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs144334309	chr3:145526693-145526694	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs4128174	chr3:145526713-145526714	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs6440391	chr3:145526763-145526764	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs116463965	chr3:145526802-145526803	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs557804080	chr3:145526805-145526806	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs373377496	chr3:145526819-145526820	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs535098386	chr3:145526844-145526845	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs552785528	chr3:145526853-145526854	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs577408760	chr3:145526893-145526894	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs538595732	chr3:145526943-145526944	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs556841778	chr3:145526944-145526945	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs28651388	chr3:145526958-145526959	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:59)

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
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	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
Chronic lymphocytic leukemia	21546498	CNVD
Basal cell lymphoma	21115979	CNVD
Colorectal cancer	18645599	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Hepatocellular carcinoma	16750200	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Blepharophimosis-ptosis-epicanthus inversus syndrome	22067867	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
abnormal development	18461090	CNVD
Breast cancer	21364760	CNVD
Mental retardation	17847001	CNVD
Basal cell lymphoma	17170743	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Autism	18923514	CNVD
Autism	22241247	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Autism	21956041	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Breast cancer	16608533	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	21509527	CNVD
Bipolar disorder	19114987	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Schizophrenia	23813976	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:200 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145525400-145526200	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr3:145525400-145527600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr3:145525600-145526800	Enhancers	Fetal Heart	heart
4	chr3:145525800-145526200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:145525800-145526600	Enhancers	Ovary	ovary
6	chr3:145526000-145526200	Enhancers	HSMM	muscle
7	chr3:145526200-145532600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:145531400-145531600	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr3:145531800-145533200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:145532600-145533200	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr3:145532600-145534400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr3:145532600-145534800	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr3:145533200-145533400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr3:145533200-145533600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr3:145533200-145533600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr3:145533200-145534400	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr3:145533200-145534400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr3:145533400-145533800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr3:145533400-145535000	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr3:145533600-145534000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr3:145533600-145535000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr3:145533800-145536000	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr3:145534000-145534200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr3:145534200-145535000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr3:145535000-145535800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr3:145535800-145536200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr3:145559800-145561600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:145564600-145565600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:145567000-145567800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:145567800-145575800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:145575600-145576400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:145575800-145576200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:145576200-145583200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:145576400-145577600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:145577600-145577800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:145581000-145581600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr3:145581000-145583600	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr3:145581400-145582800	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr3:145581400-145582800	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr3:145581600-145583200	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:145582000-145582600	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr3:145582000-145582800	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr3:145582000-145583400	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr3:145582200-145582600	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr3:145582600-145587600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr3:145582800-145583400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:145583200-145583600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:145583200-145583600	Enhancers	Brain Hippocampus Middle	brain
49	chr3:145583200-145583800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:145583200-145583800	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links