Variant report

Variant	esv3409306
Chromosome Location	chr1:78253140-78253674
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78243869..78246123-chr1:78252401..78254474,2	K562	blood:

Variant related genes	Relation type
ENSG00000222849	chromatin interactions
ENSG00000180488	chromatin interactions

Extended variants
information (count: 17 )
Associated
traits (count: 102 )

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs187363298	chr1:78253157-78253158	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs191084745	chr1:78253212-78253213	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs1166589	chr1:78253231-78253232	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
4	rs541352167	chr1:78253234-78253235	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs180750551	chr1:78253275-78253276	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs577770173	chr1:78253283-78253284	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs545211856	chr1:78253288-78253289	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs185197154	chr1:78253310-78253311	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs189962529	chr1:78253321-78253322	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs111868708	chr1:78253326-78253327	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs138458759	chr1:78253361-78253362	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs114155831	chr1:78253407-78253408	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs528096600	chr1:78253457-78253458	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs540992024	chr1:78253493-78253494	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs141449115	chr1:78253541-78253542	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs182602261	chr1:78253601-78253602	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs559960049	chr1:78253625-78253626	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:102)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Colorectal cancer	16272173	CNVD
Wilms tumour	21544195	CNVD
Coronary Disease	20032323	CNVD
Prostate cancer	21965145	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Stargardt''s disease	17277736	CNVD
Neuroblastoma	17897457	CNVD
Uveal melanoma	21693616	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-syndromic sensorineural hearing loss	22290220	CNVD
Liposarcoma	21253554	CNVD
Breast cancer	21264507	CNVD
Acute myeloid leukemia	16864856	CNVD
Astrocytoma	17387387	CNVD
Cancer	21499728	CNVD
Glioblastoma multiforme	17387387	CNVD
Oligodendroglial tumors	17285580	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Neuroblastoma	17535989	CNVD
Pheochromocytoma	17535989	CNVD
Prostate cancer	16705090	CNVD
Astrocytoma	17934521	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Gastrointestinal stromal cancer	17535989	CNVD
Neuroblastoma	17533364	CNVD
Paraganglioma	17535989	CNVD
Pulmonary chondroma	17535989	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	22495311	CNVD
Non-small cell lung cancer	21385341	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Chordoma	21602918	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Melanoma	18172304	CNVD
Multiple myeloma	16461302	CNVD
Melanoma	17363583	CNVD
Cancer	21129771	CNVD
Autosomal dominant nocturnal frontal lobe epilepsy	18472482	CNVD
Hirschsprung''s Disease	21712996	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Thrombocytopenia-absent radius syndrome	21933853	CNVD
Psychiatric disorder	22848183	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Hepatocellular carcinoma	16750200	CNVD
Burkitt''s lymphoma	18698080	CNVD
Breast cancer	20409316	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Lung cancer	18438408	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17393978	CNVD
Cervical cancer	21062161	CNVD
Cancer	21183584	CNVD
Breast cancer	21785460	CNVD
Breast cancer	21364760	CNVD
Rett syndrome	21593744	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	16608533	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	17133270	CNVD
Type 2 diabetes	21956041	CNVD
Uveal melanoma	20484589	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Ewing''s sarcoma	17952124	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Poland''s syndrome	22110015	CNVD
Glioblastoma multiforme	22286061	CNVD
Glioblastoma multiforme	21922591	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Cancer	22429812	CNVD
Effusion lymphoma	18079361	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Colorectal cancer	16774939	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:139 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78246000-78265800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:78246000-78265800	Weak transcription	Pancreas	Pancrea
3	chr1:78246000-78284200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:78246000-78285600	Weak transcription	Colonic Mucosa	Colon
5	chr1:78246200-78254000	Weak transcription	HSMMtube	muscle
6	chr1:78246200-78272000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:78246200-78272800	Weak transcription	Psoas Muscle	Psoas
8	chr1:78246200-78279400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:78246200-78279600	Weak transcription	Aorta	Aorta
10	chr1:78246400-78254200	Weak transcription	NH-A	brain
11	chr1:78246400-78272400	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr1:78246400-78273200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:78246400-78274000	Weak transcription	Fetal Kidney	kidney
14	chr1:78246400-78287400	Weak transcription	Fetal Heart	heart
15	chr1:78246600-78274200	Weak transcription	HMEC	breast
16	chr1:78247400-78278400	Weak transcription	Hela-S3	cervix
17	chr1:78247600-78254000	Weak transcription	Fetal Brain Male	brain
18	chr1:78247600-78262200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:78247600-78272400	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:78247800-78257600	Weak transcription	NHDF-Ad	bronchial
21	chr1:78248000-78260000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:78248600-78288200	Weak transcription	Small Intestine	intestine
23	chr1:78248800-78256800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:78249000-78253200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:78249000-78254600	Strong transcription	Primary B cells from cord blood	blood
26	chr1:78249000-78256600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr1:78249000-78257600	Weak transcription	HepG2	liver
28	chr1:78249000-78259200	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:78249200-78254400	Weak transcription	Stomach Mucosa	stomach
30	chr1:78249200-78256800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:78249200-78271400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:78249400-78253200	Strong transcription	Ovary	ovary
33	chr1:78249400-78253400	Strong transcription	Fetal Muscle Leg	muscle
34	chr1:78249400-78253400	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr1:78249400-78254600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr1:78249400-78255000	Strong transcription	Primary B cells from peripheral blood	blood
37	chr1:78249400-78255200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:78249400-78256600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:78249400-78257000	Strong transcription	Primary T cells from cord blood	blood
40	chr1:78249400-78257600	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr1:78249600-78253200	Strong transcription	Fetal Brain Female	brain
42	chr1:78249600-78254600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:78249600-78255200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:78249600-78255600	Strong transcription	Fetal Muscle Trunk	muscle
45	chr1:78249600-78256000	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr1:78249600-78257200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:78249600-78257200	Strong transcription	Adipose Nuclei	Adipose
48	chr1:78249600-78258200	Strong transcription	Fetal Thymus	thymus
49	chr1:78249800-78265200	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr1:78250000-78253200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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