Variant report

Variant	esv3404114
Chromosome Location	chr1:224004579-224005727
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	STAT3	chr1:224005149-224005268	MCF10A-Er-Src	breast:	n/a	n/a
2	ZNF263	chr1:224004633-224004913	HEK293-T-REx	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223999460..224001439-chr1:224004268..224006826,2	K562	blood:
2	chr1:224000840..224004910-chr1:224006824..224010402,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CAPN2-2	chr1:224005645-224006568	NONHSAT009743

Variant related genes	Relation type
TP53BP2	TF binding region
ENSG00000143514	chromatin interactions

Extended variants
information (count: 32 )
Associated
traits (count: 95 )

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs556221418	chr1:224004649-224004650	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs570803428	chr1:224004670-224004671	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs535033702	chr1:224004679-224004680	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs553515307	chr1:224004693-224004694	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs369737490	chr1:224004694-224004695	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs542279840	chr1:224004790-224004791	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs115136918	chr1:224004909-224004910	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs71644751	chr1:224004934-224004935	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs71644752	chr1:224004942-224004943	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs12760255	chr1:224004945-224004946	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs575669792	chr1:224004959-224004960	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs546210779	chr1:224004960-224004961	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs373389394	chr1:224005119-224005120	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs564519090	chr1:224005188-224005189	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs575625687	chr1:224005275-224005276	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs532416493	chr1:224005337-224005338	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs376804021	chr1:224005342-224005343	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs115597041	chr1:224005345-224005346	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs7543815	chr1:224005353-224005354	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs61823580	chr1:224005398-224005399	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs547838471	chr1:224005454-224005455	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs569401033	chr1:224005472-224005473	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs530563855	chr1:224005521-224005522	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs532999160	chr1:224005532-224005533	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs551731294	chr1:224005536-224005537	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs7536779	chr1:224005545-224005546	Weak transcription Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs144358677	chr1:224005573-224005574	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs77664564	chr1:224005627-224005628	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs535289985	chr1:224005646-224005647	Weak transcription Strong transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs183976770	chr1:224005649-224005650	Weak transcription Strong transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
31	rs73127450	chr1:224005718-224005719	Weak transcription Strong transcription Genic enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs560712844	chr1:224005726-224005727	Weak transcription Strong transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:95)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Medulloblastoma	21979893	CNVD
Cancer	20164919	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Liposarcoma	21253554	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	21899760	CNVD
Breast cancer	21858162	CNVD
Non-small cell lung cancer	21385341	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chordoma	18071362	CNVD
T-cell lymphomas	19863542	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Lung cancer	18438408	CNVD
Medulloblastoma	16783165	CNVD
Basal cell lymphoma	17170743	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Mental retardation	19951919	CNVD
Non-syndromic sensorineural hearing loss	17873649	CNVD
Acute myeloid leukemia	17268525	CNVD
Lung cancer	16740712	CNVD
Renal cell carcinoma	18765545	CNVD
Basal cell lymphoma	17053054	CNVD
Developmental delay	21147756	CNVD
Autism	14699429	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Autism	20808228	CNVD
Fumarase deficiency	21572526	CNVD
Autism	17483303	CNVD
Kartagener syndrome	16639409	CNVD
Congenital abnormalities	21549014	CNVD
Developmental delay	21549014	CNVD
Mental retardation	21549014	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Liver carcinoma	19366792	CNVD
Leukoplakia	24403051	CNVD
Congenital diaphragmatic hernia	21525063	CNVD
Glioblastoma multiforme	21138945	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Cancer	20164920	CNVD

Chromatin state (count:162 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223956600-224004600	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr1:223956600-224004600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:223960200-224025400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:223964400-224008000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:223988200-224012000	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:223990600-224007000	Weak transcription	Fetal Brain Male	brain
7	chr1:223991200-224007400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:223991200-224007400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:223991200-224010800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:223991400-224007600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:223993400-224008400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:223994600-224007000	Weak transcription	Colonic Mucosa	Colon
13	chr1:223994600-224008200	Weak transcription	Psoas Muscle	Psoas
14	chr1:223995800-224009400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:223996000-224007600	Weak transcription	Hela-S3	cervix
16	chr1:223997200-224004600	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr1:223999600-224007800	Weak transcription	Brain Angular Gyrus	brain
18	chr1:223999800-224004800	Strong transcription	Fetal Intestine Large	intestine
19	chr1:223999800-224010800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:224000200-224007400	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:224001000-224010000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:224001400-224007600	Weak transcription	Brain Germinal Matrix	brain
23	chr1:224001400-224008400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:224001600-224006800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:224001800-224010600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:224001800-224010800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr1:224002000-224005600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr1:224002000-224005800	Weak transcription	Fetal Stomach	stomach
29	chr1:224002000-224006800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:224002000-224006800	Weak transcription	Adipose Nuclei	Adipose
31	chr1:224002000-224006800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:224002000-224007600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:224002000-224007600	Weak transcription	Fetal Kidney	kidney
34	chr1:224002000-224007600	Weak transcription	Lung	lung
35	chr1:224002000-224007600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr1:224002000-224008200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:224002000-224008200	Weak transcription	Spleen	Spleen
38	chr1:224002000-224008400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:224002000-224015000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:224002000-224023800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:224002200-224005400	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:224002200-224005600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:224002200-224005600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:224002200-224005600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:224002200-224006800	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr1:224002200-224007000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr1:224002200-224007000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:224002200-224007000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:224002200-224007200	Weak transcription	Fetal Brain Female	brain
50	chr1:224002200-224007600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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