Variant report

Variant	esv3357285
Chromosome Location	chr3:23995884-23996476
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	POLR2A	chr3:23996142-23996211	A549	lung:	n/a	n/a
2	POLR2A	chr3:23994885-23996788	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:23957572..23960051-chr3:23995970..23999234,5	MCF-7	breast:
2	chr3:23956080..23959048-chr3:23995915..23997492,2	MCF-7	breast:
3	chr3:23985538..23993367-chr3:23993730..24003801,19	MCF-7	breast:

Variant related genes	Relation type
NR1D2	TF binding region
ENSG00000197885	chromatin interactions
ENSG00000174748	chromatin interactions
ENSG00000174738	chromatin interactions

Extended variants
information (count: 27 )
Associated
traits (count: 71 )

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs142359214	chr3:23995936-23995937	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
2	rs113335852	chr3:23995958-23995959	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
3	rs190109204	chr3:23995973-23995974	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs559492799	chr3:23995993-23995994	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs530105390	chr3:23996010-23996011	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs72627099	chr3:23996013-23996014	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs563426139	chr3:23996014-23996015	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
8	rs181813342	chr3:23996019-23996020	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
9	rs72627100	chr3:23996056-23996057	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs367555924	chr3:23996065-23996066	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
11	rs17854365	chr3:23996073-23996074	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
12	rs563905774	chr3:23996108-23996109	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
13	rs371828572	chr3:23996119-23996120	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs528383367	chr3:23996144-23996145	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs143811972	chr3:23996184-23996185	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs201515529	chr3:23996189-23996190	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs143411191	chr3:23996191-23996192	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs568010643	chr3:23996196-23996197	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs141523313	chr3:23996224-23996225	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs147325599	chr3:23996307-23996308	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs200661316	chr3:23996313-23996314	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs202032439	chr3:23996326-23996327	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs374331352	chr3:23996337-23996338	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
24	rs4858095	chr3:23996371-23996372	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
25	rs4858096	chr3:23996397-23996398	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs539510617	chr3:23996403-23996404	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
27	rs6788473	chr3:23996472-23996473	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:71)

Disease	PMID	Source
Esophageal squamous carcinoma	18405350	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
lymphocytic leukemia	21291569	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Esophageal cancer	20955586	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Myelofibrosis	22110671	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:181 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23988200-24000600	Weak transcription	Fetal Brain Male	brain
2	chr3:23988200-24003600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:23988400-23996000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:23988400-23996400	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr3:23988400-24003000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr3:23988400-24003400	Weak transcription	Fetal Kidney	kidney
7	chr3:23988600-23996000	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr3:23989000-23996400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:23989000-23997800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:23989000-23998200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:23989200-23996000	Enhancers	Adipose Nuclei	Adipose
12	chr3:23989200-23996200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:23989200-23996200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:23989200-24000600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:23989200-24003000	Weak transcription	Fetal Thymus	thymus
16	chr3:23989200-24007400	Weak transcription	Fetal Brain Female	brain
17	chr3:23989200-24018000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:23989200-24020600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:23989200-24033200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:23989400-23996000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:23989400-23996200	Enhancers	Brain Hippocampus Middle	brain
22	chr3:23989600-24003400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr3:23989600-24003400	Weak transcription	Esophagus	oesophagus
24	chr3:23989600-24003600	Weak transcription	Colonic Mucosa	Colon
25	chr3:23989800-23996000	Weak transcription	Osteobl	bone
26	chr3:23989800-24017800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:23990000-24000200	Weak transcription	HUVEC	blood vessel
28	chr3:23990000-24001000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:23990400-23996200	Weak transcription	Placenta	Placenta
30	chr3:23990400-23997600	Weak transcription	NH-A	brain
31	chr3:23990600-23999800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:23991000-23996000	Enhancers	Primary B cells from peripheral blood	blood
33	chr3:23991000-23996400	Enhancers	Brain Cingulate Gyrus	brain
34	chr3:23991400-23996000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:23991600-23996000	Enhancers	Colon Smooth Muscle	Colon
36	chr3:23991600-23996200	Weak transcription	Fetal Muscle Leg	muscle
37	chr3:23991800-23996200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:23991800-23996200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr3:23991800-23996400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr3:23991800-23999600	Weak transcription	HSMMtube	muscle
41	chr3:23992000-23996000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr3:23992000-23996000	Weak transcription	Hela-S3	cervix
43	chr3:23992000-23996000	Weak transcription	HSMM	muscle
44	chr3:23992000-23996200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:23992000-23996400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:23992000-24000000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:23992000-24001600	Weak transcription	Fetal Stomach	stomach
48	chr3:23992000-24007400	Weak transcription	Thymus	Thymus
49	chr3:23992200-23996000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr3:23992200-23996000	Enhancers	Primary T helper cells PMA-I stimulated	--

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