Variant report

Variant	esv2508330
Chromosome Location	chr1:224565641-224567115
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	chr1:224565954..224567779-chr1:224572206..224574847,2	K562	blood:
2	chr1:224550099..224552705-chr1:224565403..224568845,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNIH4-1	chr1:224566771-224567161	NONHSAT009796

Extended variants
information (count: 39 )
Associated
traits (count: 93 )

Variant overlapped rSNPs/rCNVs (count:39 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs555212248	chr1:224565733-224565734	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
2	rs200873689	chr1:224565753-224565754	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs61376551	chr1:224565755-224565756	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs60063902	chr1:224565769-224565770	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs545007986	chr1:224565780-224565781	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs577089012	chr1:224565802-224565803	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs6701145	chr1:224565821-224565822	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
8	rs577247684	chr1:224565824-224565825	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs541454066	chr1:224565843-224565844	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
10	rs61000820	chr1:224565885-224565886	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs527582528	chr1:224565891-224565892	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
12	rs542471523	chr1:224565954-224565955	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
13	rs183733077	chr1:224566023-224566024	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs116500608	chr1:224566039-224566040	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs549694626	chr1:224566089-224566090	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs553310980	chr1:224566154-224566155	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs561391232	chr1:224566179-224566180	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs11586729	chr1:224566216-224566217	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
19	rs56308617	chr1:224566271-224566272	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs532107200	chr1:224566283-224566284	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs55936364	chr1:224566307-224566308	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs547373468	chr1:224566577-224566578	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs12135852	chr1:224566654-224566655	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
24	rs565640871	chr1:224566691-224566692	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
25	rs371860118	chr1:224566717-224566718	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
26	rs200306692	chr1:224566784-224566785	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
27	rs149125195	chr1:224566789-224566790	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
28	rs188007583	chr1:224566805-224566806	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
29	rs373829232	chr1:224566806-224566807	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
30	rs570344591	chr1:224566810-224566811	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
31	rs192279478	chr1:224566855-224566856	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
32	rs77770374	chr1:224566921-224566922	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
33	rs573343321	chr1:224566931-224566932	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
34	rs577313325	chr1:224566968-224566969	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
35	rs182702979	chr1:224566975-224566976	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
36	rs4654037	chr1:224567004-224567005	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
37	rs574457869	chr1:224567011-224567012	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
38	rs372410465	chr1:224567045-224567046	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
39	rs376679830	chr1:224567098-224567099	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:93)

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
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
Cancer	17060936	CNVD

Chromatin state (count:211 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224545800-224605000	Weak transcription	Aorta	Aorta
2	chr1:224547000-224593200	Weak transcription	Stomach Mucosa	stomach
3	chr1:224547400-224618600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:224547800-224568600	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:224548000-224576000	Weak transcription	Fetal Brain Male	brain
6	chr1:224550400-224568000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:224551000-224568000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:224551200-224565800	Strong transcription	Primary B cells from cord blood	blood
9	chr1:224551400-224568600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:224551600-224566600	Strong transcription	Dnd41	blood
11	chr1:224551600-224568000	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:224551600-224568400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:224552800-224565800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:224553200-224567400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:224553400-224567000	Strong transcription	Adipose Nuclei	Adipose
16	chr1:224553400-224567400	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr1:224553600-224566000	Strong transcription	Fetal Intestine Large	intestine
18	chr1:224553600-224566400	Strong transcription	Fetal Intestine Small	intestine
19	chr1:224553800-224568800	Strong transcription	Fetal Stomach	stomach
20	chr1:224554400-224568200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr1:224554600-224567200	Strong transcription	Liver	Liver
22	chr1:224554600-224567400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:224554800-224568600	Strong transcription	Fetal Brain Female	brain
24	chr1:224555000-224568000	Strong transcription	Brain Anterior Caudate	brain
25	chr1:224555000-224568200	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr1:224555200-224566000	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr1:224555200-224568000	Strong transcription	Brain Germinal Matrix	brain
28	chr1:224555800-224581400	Weak transcription	Fetal Heart	heart
29	chr1:224556000-224591000	Weak transcription	Small Intestine	intestine
30	chr1:224558200-224567200	Strong transcription	A549	lung
31	chr1:224560600-224567800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr1:224561000-224566000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
33	chr1:224561000-224567000	Strong transcription	Lung	lung
34	chr1:224561600-224567000	Strong transcription	Thymus	Thymus
35	chr1:224561800-224567400	Strong transcription	Fetal Kidney	kidney
36	chr1:224562000-224567000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr1:224562400-224566200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:224562600-224567400	Strong transcription	Fetal Lung	lung
39	chr1:224562800-224565800	Genic enhancers	HSMM	muscle
40	chr1:224562800-224566200	Genic enhancers	Fetal Thymus	thymus
41	chr1:224562800-224569600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:224563000-224577200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr1:224563000-224593400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:224563200-224567400	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:224563200-224568600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:224563400-224567400	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr1:224563600-224566200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:224563600-224568000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:224563600-224568200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:224563600-224568600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links