Variant report

Variant	esv2476939
Chromosome Location	chr1:227451633-227453112
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	GATA3	chr1:227452110-227452141	SH-SY5Y	brain:	n/a	n/a
2	POLR2A	chr1:227453109-227453274	A549	lung:	n/a	n/a
3	TBL1XR1	chr1:227451937-227451956	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227446907..227449535-chr1:227450206..227452004,2	K562	blood:
2	chr1:227441285..227444497-chr1:227452902..227455834,3	K562	blood:

Variant related genes	Relation type
ENSG00000236636	TF binding region
ENSG00000143776	chromatin interactions

Extended variants
information (count: 56 )
Associated
traits (count: 91 )

Variant overlapped rSNPs/rCNVs (count:56 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs561211861	chr1:227451645-227451646	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs576462289	chr1:227451673-227451674	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs529837937	chr1:227451705-227451706	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs189147756	chr1:227451710-227451711	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs372618173	chr1:227451719-227451720	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs114836371	chr1:227451736-227451737	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs117440870	chr1:227451782-227451783	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs533647054	chr1:227451790-227451791	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs557534888	chr1:227451802-227451803	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs575583063	chr1:227451811-227451812	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs4354510	chr1:227451815-227451816	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs569627854	chr1:227451823-227451824	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs564383620	chr1:227451851-227451852	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs528397606	chr1:227451880-227451881	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs540002963	chr1:227451884-227451885	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs561555009	chr1:227451887-227451888	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs529100233	chr1:227451950-227451951	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs550253897	chr1:227451981-227451982	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs538698291	chr1:227451994-227451995	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs4375224	chr1:227452040-227452041	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs532919932	chr1:227452051-227452052	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs565290659	chr1:227452087-227452088	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs181906209	chr1:227452181-227452182	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs2670469	chr1:227452224-227452225	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs571094153	chr1:227452266-227452267	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs535019274	chr1:227452290-227452291	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs547171108	chr1:227452356-227452357	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs568664913	chr1:227452358-227452359	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs2718214	chr1:227452359-227452360	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs543856940	chr1:227452461-227452462	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs374969578	chr1:227452542-227452543	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs201840755	chr1:227452560-227452561	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs574310821	chr1:227452561-227452562	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs185736274	chr1:227452590-227452591	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs539791846	chr1:227452601-227452602	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs536426117	chr1:227452606-227452607	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs557883045	chr1:227452619-227452620	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs573050819	chr1:227452643-227452644	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs540139496	chr1:227452695-227452696	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs561689890	chr1:227452697-227452698	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs1969230	chr1:227452700-227452701	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
42	rs544030896	chr1:227452716-227452717	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs562576247	chr1:227452720-227452721	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs576580452	chr1:227452732-227452733	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs1533283	chr1:227452751-227452752	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs2670470	chr1:227452844-227452845	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs559898874	chr1:227452864-227452865	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs11800169	chr1:227452952-227452953	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
49	rs11808613	chr1:227452963-227452964	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs541475599	chr1:227453001-227453002	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	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
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
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
Breast cancer	22522925	CNVD

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227414000-227459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:227414200-227453800	Weak transcription	HSMM	muscle
3	chr1:227415800-227456800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:227431600-227486200	Weak transcription	NHDF-Ad	bronchial
5	chr1:227432000-227459200	Weak transcription	Fetal Lung	lung
6	chr1:227432200-227455400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:227432800-227455600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:227433000-227469000	Weak transcription	Aorta	Aorta
9	chr1:227433200-227452800	Weak transcription	Ovary	ovary
10	chr1:227434000-227453400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:227434200-227455400	Weak transcription	Left Ventricle	heart
12	chr1:227434200-227455400	Weak transcription	Right Ventricle	heart
13	chr1:227434200-227455800	Weak transcription	Adipose Nuclei	Adipose
14	chr1:227434600-227468800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:227434800-227458400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:227435000-227457000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:227435600-227453600	Weak transcription	Fetal Intestine Small	intestine
18	chr1:227440000-227456600	Weak transcription	HepG2	liver
19	chr1:227440200-227456800	Weak transcription	HUVEC	blood vessel
20	chr1:227441800-227452000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:227443400-227474000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:227445800-227458400	Weak transcription	NHEK	skin
23	chr1:227447000-227456800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:227447200-227452600	Weak transcription	Brain Substantia Nigra	brain
25	chr1:227447200-227473600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:227447400-227452800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:227447400-227455000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:227448400-227452400	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:227448400-227453600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:227448400-227456400	Weak transcription	Psoas Muscle	Psoas
31	chr1:227448600-227457200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr1:227449600-227452800	Weak transcription	Brain Anterior Caudate	brain
33	chr1:227449600-227473600	Weak transcription	NH-A	brain
34	chr1:227449800-227453600	Weak transcription	Colon Smooth Muscle	Colon
35	chr1:227449800-227465200	Weak transcription	K562	blood
36	chr1:227451200-227452000	Enhancers	Brain Angular Gyrus	brain
37	chr1:227452000-227452800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:227452000-227452800	Weak transcription	Brain Angular Gyrus	brain
39	chr1:227452400-227456000	Enhancers	Brain Hippocampus Middle	brain
40	chr1:227452600-227453200	Enhancers	Brain Substantia Nigra	brain
41	chr1:227452800-227453000	Enhancers	Brain Angular Gyrus	brain
42	chr1:227452800-227453000	Enhancers	Brain Anterior Caudate	brain
43	chr1:227452800-227453000	Enhancers	Brain Cingulate Gyrus	brain
44	chr1:227452800-227453000	Enhancers	Lung	lung
45	chr1:227452800-227453400	Enhancers	Ovary	ovary
46	chr1:227452800-227453800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:227452800-227454400	Weak transcription	Stomach Mucosa	stomach
48	chr1:227452800-227463800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:227453000-227453400	Weak transcription	Brain Angular Gyrus	brain
50	chr1:227453000-227453400	Weak transcription	Brain Anterior Caudate	brain

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