Variant report

Variant	esv3387925
Chromosome Location	chr3:100056362-100059860
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:62)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GTF2F1	chr3:100057680-100057704	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:100056720-100057772	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:100056941-100056973	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr3:100057663-100057778	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr3:100057219-100057289	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr3:100057025-100057182	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:100057204-100057690	GM12878	blood:	n/a	n/a
8	RCOR1	chr3:100057784-100057973	K562	blood:	n/a	n/a
9	STAT3	chr3:100059488-100059574	GM12878	blood:	n/a	n/a

(count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:100057581-100057631	AG04449	skin:	fetal
2	chr3:100057581-100057631	AG04449	skin:	fetal
3	chr3:100057581-100057631	A549	lung:	n/a
4	chr3:100057581-100057631	AG10803	skin:	n/a
5	chr3:100057581-100057631	HCT-116	colon:	n/a
6	chr3:100057581-100057631	HNPCEpiC	eye:	n/a
7	chr3:100057581-100057631	HAEpiC	amniotic membrane:	n/a
8	chr3:100057581-100057631	ovcar-3	ovarian:	n/a
9	chr3:100057581-100057631	AG04450	lung:	fetal
10	chr3:100057581-100057631	HUVEC	blood vessel:	n/a
11	chr3:100057581-100057631	T-47D	breast:	n/a
12	chr3:100057581-100057631	Jurkat	blood:	n/a
13	chr3:100057581-100057631	HCF	heart:	n/a
14	chr3:100057581-100057631	PrEC	prostate:	n/a
15	chr3:100057581-100057631	HEK293	kidney:	embryo
16	chr3:100057581-100057631	HRCEpiC	kidney:	n/a
17	chr3:100057581-100057631	SK-N-MC	brain:	n/a
18	chr3:100057581-100057631	GM12892	blood:	n/a
19	chr3:100057581-100057631	ProgFib	skin:	n/a
20	chr3:100057581-100057631	PANC-1	pancreas:	n/a
21	chr3:100057581-100057631	AG09309	skin:	n/a
22	chr3:100057581-100057631	HMEC	breast:	n/a
23	chr3:100057581-100057631	BJ	skin:	n/a
24	chr3:100057581-100057631	SAEC	small airway:	n/a
25	chr3:100057581-100057631	HRE	kidney:	n/a
26	chr3:100057581-100057631	MCF10A-Er-Src	breast:	n/a
27	chr3:100057581-100057631	HCPEpiC	choroid plexus:	n/a
28	chr3:100057581-100057631	U87	brain:	n/a
29	chr3:100057581-100057631	BE2_C	brain:	n/a
30	chr3:100057581-100057631	NT2-D1	testis:	n/a
31	chr3:100057581-100057631	ECC-1	luminal epithelium:	n/a
32	chr3:100057581-100057631	SKMC	muscle:	n/a
33	chr3:100057581-100057631	GM12891	blood:	n/a
34	chr3:100057581-100057631	SK-N-SH_RA	brain:	n/a
35	chr3:100057581-100057631	AoSMC	blood vessel:	n/a
36	chr3:100057581-100057631	RPTEC	kidney:	n/a
37	chr3:100057581-100057631	Caco-2	colon:	n/a
38	chr3:100057581-100057631	NHDF-neo	bronchial:	n/a
39	chr3:100057581-100057631	SK-N-SH	brain:	n/a
40	chr3:100057581-100057631	NH-A	brain:	n/a
41	chr3:100057581-100057631	HCM	heart:	n/a
42	chr3:100057581-100057631	GM06990	blood:	n/a
43	chr3:100057581-100057631	HIPEpiC	eye:	n/a
44	chr3:100057581-100057631	AG09319	gingival:	n/a
45	chr3:100057581-100057631	Hepatocyte	liver:	n/a
46	chr3:100057581-100057631	PFSK-1	brain:	n/a
47	chr3:100057581-100057631	IMR90	lung:	fetal
48	chr3:100057581-100057631	H1-hESC	embryonic stem cell:	embryo
49	chr3:100057581-100057631	CMK	blood:	n/a
50	chr3:100057581-100057631	HepG2	liver:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:100055925..100057917-chr3:100076174..100079116,2	MCF-7	breast:
2	chr3:100058351..100061697-chr3:100061751..100064533,3	MCF-7	breast:
3	chr3:100055058..100056849-chr3:100060980..100063043,2	MCF-7	breast:
4	chr3:100051539..100055958-chr3:100056037..100061247,9	MCF-7	breast:
5	chr3:100056838..100058599-chr3:100119834..100121558,2	MCF-7	breast:

No data

Variant related genes	Relation type
NIT2	TF binding region
NIT2	CpG island
ENSG00000154174	chromatin interactions
ENSG00000114021	chromatin interactions
ENSG00000206535	chromatin interactions

Extended variants
information (count: 162 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:162 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs532628421	chr3:100056371-100056372	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs541555373	chr3:100056385-100056386	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs559744976	chr3:100056476-100056477	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs530047413	chr3:100056487-100056488	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs277622	chr3:100056499-100056500	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs570244742	chr3:100056500-100056501	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs531270815	chr3:100056516-100056517	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs552474491	chr3:100056551-100056552	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs570734372	chr3:100056552-100056553	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs139347500	chr3:100056592-100056593	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs113508423	chr3:100056609-100056610	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs565290521	chr3:100056615-100056616	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs34745815	chr3:100056616-100056617	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs554587371	chr3:100056661-100056662	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs574313908	chr3:100056686-100056687	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs143257219	chr3:100056772-100056773	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs537377918	chr3:100056773-100056774	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs558754938	chr3:100056787-100056788	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs577123251	chr3:100056814-100056815	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs541492020	chr3:100056845-100056846	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
21	rs566787776	chr3:100056849-100056850	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
22	rs144791580	chr3:100056893-100056894	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
23	rs402870	chr3:100056894-100056895	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs563730364	chr3:100056963-100056964	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
25	rs559357635	chr3:100056989-100056990	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
26	rs111389443	chr3:100056994-100056995	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
27	rs183769775	chr3:100057000-100057001	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
28	rs552468491	chr3:100057007-100057008	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
29	rs564299146	chr3:100057029-100057030	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
30	rs186326668	chr3:100057053-100057054	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
31	rs34409241	chr3:100057062-100057063	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
32	rs190418981	chr3:100057091-100057092	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
33	rs72941434	chr3:100057109-100057110	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs114208385	chr3:100057124-100057125	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
35	rs277621	chr3:100057203-100057204	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
36	rs277620	chr3:100057269-100057270	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs182132295	chr3:100057279-100057280	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
38	rs114866291	chr3:100057338-100057339	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
39	rs185722	chr3:100057378-100057379	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
40	rs432715	chr3:100057417-100057418	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs534803441	chr3:100057482-100057483	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
42	rs148547960	chr3:100057509-100057510	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
43	rs574816978	chr3:100057511-100057512	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
44	rs186811726	chr3:100057577-100057578	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
45	rs563501562	chr3:100057603-100057604	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
46	rs548285929	chr3:100057634-100057635	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
47	rs575603458	chr3:100057645-100057646	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
48	rs41272637	chr3:100057651-100057652	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
49	rs546039354	chr3:100057658-100057659	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
50	rs41272639	chr3:100057670-100057671	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:57)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Renal cell carcinoma	21668985	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Neurodevelopmental disorder	22521361	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	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
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
small cell lung cancer	20016488	CNVD
Ductal carcinoma	22052326	CNVD
Myelofibrosis	22110671	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Breast cancer	16608533	CNVD
Amyotrophic lateral sclerosis	20685689	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:237 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100054000-100065000	Weak transcription	Spleen	Spleen
2	chr3:100054200-100081000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:100054400-100067600	Weak transcription	Psoas Muscle	Psoas
4	chr3:100054600-100056600	Enhancers	Fetal Intestine Small	intestine
5	chr3:100054600-100057000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:100054600-100057000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:100054600-100057200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:100054600-100057200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:100054600-100057400	Weak transcription	Primary T cells from cord blood	blood
10	chr3:100054600-100058000	Weak transcription	Fetal Brain Male	brain
11	chr3:100054600-100058000	Weak transcription	Fetal Brain Female	brain
12	chr3:100054600-100058200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr3:100054600-100058400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:100054600-100058600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:100054600-100058600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:100054600-100058800	Weak transcription	Aorta	Aorta
17	chr3:100054600-100059400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:100054600-100059800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:100054600-100060200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:100054600-100063000	Weak transcription	Brain Substantia Nigra	brain
21	chr3:100054600-100064200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:100054600-100064400	Weak transcription	Thymus	Thymus
23	chr3:100054600-100102600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr3:100054800-100056600	Weak transcription	Fetal Stomach	stomach
25	chr3:100054800-100057000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:100054800-100057000	Weak transcription	Fetal Lung	lung
27	chr3:100054800-100057000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr3:100054800-100057200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:100054800-100057200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:100054800-100057200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:100054800-100057200	Weak transcription	Primary B cells from cord blood	blood
32	chr3:100054800-100057200	Weak transcription	HSMM	muscle
33	chr3:100054800-100057200	Weak transcription	Osteobl	bone
34	chr3:100054800-100057400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:100054800-100057400	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr3:100054800-100057600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr3:100054800-100057600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:100054800-100057600	Weak transcription	Adipose Nuclei	Adipose
39	chr3:100054800-100057600	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:100054800-100057600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr3:100054800-100057800	Enhancers	Liver	Liver
42	chr3:100054800-100057800	Weak transcription	Gastric	stomach
43	chr3:100054800-100057800	Weak transcription	Ovary	ovary
44	chr3:100054800-100057800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr3:100054800-100057800	Weak transcription	NHDF-Ad	bronchial
46	chr3:100054800-100058000	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr3:100054800-100058000	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr3:100054800-100058000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:100054800-100058000	Weak transcription	Fetal Thymus	thymus
50	chr3:100054800-100058000	Weak transcription	Left Ventricle	heart

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