Variant report

Variant	esv3339932
Chromosome Location	chr1:227982579-227984177
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	chr1:227976724..227980772-chr1:227980865..227984605,4	MCF-7	breast:
2	chr1:227977112..227980203-chr1:227982448..227986232,4	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 91 )

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs536846088	chr1:227982579-227982580	Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs575676202	chr1:227982589-227982590	Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs556658819	chr1:227982591-227982592	Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs61826979	chr1:227982605-227982606	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs546315345	chr1:227982607-227982608	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs558223606	chr1:227982638-227982639	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs576478592	chr1:227982658-227982659	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs113636050	chr1:227982726-227982727	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs181047303	chr1:227982730-227982731	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs115372206	chr1:227982752-227982753	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs529173791	chr1:227982780-227982781	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs544106834	chr1:227982808-227982809	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
13	rs535206698	chr1:227982830-227982831	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
14	rs532906258	chr1:227982834-227982835	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
15	rs112364957	chr1:227982936-227982937	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
16	rs12123959	chr1:227982968-227982969	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
17	rs527263148	chr1:227982997-227982998	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
18	rs547285984	chr1:227983011-227983012	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
19	rs191155722	chr1:227983142-227983143	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
20	rs183311387	chr1:227983199-227983200	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
21	rs187557428	chr1:227983267-227983268	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
22	rs372438792	chr1:227983304-227983305	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
23	rs560859944	chr1:227983315-227983316	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
24	rs191457949	chr1:227983336-227983337	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
25	rs539942937	chr1:227983399-227983400	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
26	rs558256100	chr1:227983411-227983412	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
27	rs573290073	chr1:227983451-227983452	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
28	rs540665750	chr1:227983472-227983473	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
29	rs555712550	chr1:227983493-227983494	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
30	rs183278663	chr1:227983498-227983499	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
31	rs12743569	chr1:227983501-227983502	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
32	rs187818046	chr1:227983559-227983560	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
33	rs544488751	chr1:227983566-227983567	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
34	rs192894147	chr1:227983677-227983678	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
35	rs532913046	chr1:227983715-227983716	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
36	rs543236199	chr1:227983716-227983717	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
37	rs4997265	chr1:227983723-227983724	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
38	rs527367917	chr1:227983726-227983727	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
39	rs548730007	chr1:227983742-227983743	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
40	rs567249785	chr1:227983749-227983750	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
41	rs115471811	chr1:227983793-227983794	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
42	rs551215147	chr1:227983814-227983815	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
43	rs569494367	chr1:227983817-227983818	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
44	rs373543565	chr1:227983863-227983864	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
45	rs184530851	chr1:227983931-227983932	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
46	rs532141622	chr1:227984099-227984100	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
47	rs73098936	chr1:227984113-227984114	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs368650964	chr1:227984128-227984129	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
49	rs534299379	chr1:227984147-227984148	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
50	rs139548628	chr1:227984176-227984177	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a

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
Non-syndromic sensorineural hearing loss	17122850	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227977000-227985000	Weak transcription	Gastric	stomach
2	chr1:227980000-227983600	Enhancers	Fetal Muscle Leg	muscle
3	chr1:227980000-227983800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
4	chr1:227980400-227982800	Enhancers	H1 Cell Line	embryonic stem cell
5	chr1:227980400-227983000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:227980600-227982600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:227980600-227982800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:227980600-227982800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:227980800-227982800	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr1:227981000-227982800	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr1:227981000-227982800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:227981000-227982800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:227981000-227982800	Enhancers	Ovary	ovary
14	chr1:227981200-227982600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:227981200-227982600	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr1:227981200-227982800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:227981200-227982800	Enhancers	HSMMtube	muscle
18	chr1:227981400-227982600	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr1:227981400-227982800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:227981400-227982800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr1:227981400-227982800	Enhancers	Colonic Mucosa	Colon
22	chr1:227981400-227982800	Enhancers	Esophagus	oesophagus
23	chr1:227981400-227982800	Enhancers	Fetal Lung	lung
24	chr1:227981400-227982800	Bivalent Enhancer	Fetal Stomach	stomach
25	chr1:227981400-227982800	Enhancers	Placenta Amnion	Placenta Amnion
26	chr1:227981400-227982800	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr1:227981600-227982800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:227981600-227982800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:227981600-227982800	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr1:227981800-227982600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:227981800-227982800	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr1:227981800-227982800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:227981800-227982800	Bivalent Enhancer	Adipose Nuclei	Adipose
34	chr1:227981800-227982800	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr1:227981800-227982800	Enhancers	Fetal Intestine Large	intestine
36	chr1:227981800-227982800	Bivalent Enhancer	Placenta	Placenta
37	chr1:227981800-227982800	Enhancers	HSMM	muscle
38	chr1:227981800-227982800	Flanking Active TSS	Osteobl	bone
39	chr1:227982000-227982600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:227982000-227982600	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr1:227982000-227982600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:227982000-227982600	Enhancers	Fetal Thymus	thymus
43	chr1:227982000-227982800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
44	chr1:227982000-227982800	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:227982000-227982800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr1:227982000-227982800	Enhancers	Rectal Smooth Muscle	rectum
47	chr1:227982000-227982800	Enhancers	Right Ventricle	heart
48	chr1:227982000-227982800	Enhancers	HMEC	breast
49	chr1:227982000-227982800	Flanking Active TSS	NHLF	lung
50	chr1:227982200-227982600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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