Variant report

Variant	esv3439428
Chromosome Location	chr1:228528245-228528414
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228525990..228529062-chr1:228536667..228539539,3	K562	blood:
2	chr1:228523292..228526039-chr1:228527019..228529476,2	MCF-7	breast:
3	chr1:228527562..228531563-chr1:228538039..228541422,5	K562	blood:
4	chr1:228527319..228529174-chr1:228643388..228645419,2	K562	blood:
5	chr1:228527728..228529697-chr1:228564611..228569014,3	MCF-7	breast:
6	chr1:228526564..228529508-chr1:228637709..228639977,2	K562	blood:
7	chr1:228527379..228529811-chr1:228531746..228535149,3	K562	blood:
8	chr1:228528381..228528953-chr1:228645146..228645771,2	K562	blood:
9	chr1:228528354..228531770-chr1:228642753..228646292,3	MCF-7	breast:
10	chr1:228528065..228528943-chr1:228643524..228644134,2	MCF-7	breast:
11	chr1:228527674..228533298-chr1:228643388..228648856,7	K562	blood:
12	chr1:228528158..228528703-chr1:228703089..228703660,2	K562	blood:
13	chr1:228528294..228529171-chr1:228659243..228660230,3	K562	blood:
14	chr1:228525657..228530496-chr1:228643263..228648636,7	MCF-7	breast:
15	chr1:228520543..228523055-chr1:228527176..228529354,3	K562	blood:
16	chr1:228527085..228530281-chr1:228640175..228642076,3	K562	blood:
17	chr1:228521555..228523351-chr1:228525829..228528676,2	K562	blood:
18	chr1:228528337..228529146-chr1:228581029..228581861,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196890	chromatin interactions
ENSG00000154358	chromatin interactions
ENSG00000181218	chromatin interactions

Extended variants
information (count: 12 )
Associated
traits (count: 91 )

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs370455962	chr1:228528251-228528252	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs561270633	chr1:228528268-228528269	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs528815428	chr1:228528276-228528277	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs542224343	chr1:228528287-228528288	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs374856455	chr1:228528295-228528296	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs200917956	chr1:228528298-228528299	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs531481460	chr1:228528304-228528305	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs551265926	chr1:228528344-228528345	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs12095133	chr1:228528347-228528348	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs375463474	chr1:228528372-228528373	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs368615719	chr1:228528385-228528386	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs1150916	chr1:228528412-228528413	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:91)

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
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
Mental retardation	19951919	CNVD
Non-syndromic sensorineural hearing loss	17873649	CNVD
Basal cell lymphoma	17053054	CNVD
Autism	14699429	CNVD
Chronic lymphocytic leukemia	21546498	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
Glioblastoma multiforme	21138945	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Cancer	20164920	CNVD
Cancer	17060936	CNVD
Myelofibrosis	22110671	CNVD
abnormal development	18461090	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Melanoma	17363583	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228504400-228529600	Weak transcription	Colonic Mucosa	Colon
2	chr1:228508800-228530200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr1:228510000-228531000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:228510000-228554600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:228510200-228531200	Weak transcription	Hela-S3	cervix
6	chr1:228511200-228530000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:228511400-228528600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:228511400-228552400	Weak transcription	Psoas Muscle	Psoas
9	chr1:228512400-228532200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:228512800-228529200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:228512800-228531400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:228512800-228532600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:228513400-228531400	Weak transcription	Fetal Kidney	kidney
14	chr1:228518800-228534200	Weak transcription	Right Atrium	heart
15	chr1:228519000-228528800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:228519200-228531400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:228520000-228528400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:228520000-228538000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
19	chr1:228520200-228531800	Strong transcription	Thymus	Thymus
20	chr1:228520200-228532000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:228520200-228532000	Strong transcription	Left Ventricle	heart
22	chr1:228520200-228538200	Strong transcription	Fetal Muscle Leg	muscle
23	chr1:228520400-228529600	Strong transcription	Fetal Intestine Small	intestine
24	chr1:228520400-228531400	Strong transcription	Right Ventricle	heart
25	chr1:228520400-228531600	Strong transcription	Fetal Stomach	stomach
26	chr1:228520400-228532400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr1:228520400-228535000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:228520400-228535200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
29	chr1:228520600-228528400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:228520600-228532000	Strong transcription	Fetal Brain Female	brain
31	chr1:228520800-228528400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:228521200-228528400	Strong transcription	Primary T cells from cord blood	blood
33	chr1:228522000-228541200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:228523400-228529200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:228524400-228530000	Strong transcription	Pancreas	Pancrea
36	chr1:228524600-228530000	Strong transcription	Dnd41	blood
37	chr1:228524800-228531600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:228525000-228530000	Strong transcription	Fetal Intestine Large	intestine
39	chr1:228525400-228528400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:228525600-228529800	Strong transcription	Spleen	Spleen
41	chr1:228525800-228529000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:228525800-228531200	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:228525800-228531400	Weak transcription	A549	lung
44	chr1:228526000-228528400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:228526400-228528400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:228526600-228529600	Strong transcription	Fetal Muscle Trunk	muscle
47	chr1:228527400-228529200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:228527400-228529200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr1:228527400-228531200	Strong transcription	Lung	lung
50	chr1:228527400-228531400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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