Variant report

Variant	esv3336770
Chromosome Location	chr1:228873688-228874112
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228870974..228874192-chr1:229289899..229293413,3	MCF-7	breast:
2	chr1:228827485..228830418-chr1:228872715..228875379,2	MCF-7	breast:
3	chr1:228872086..228874934-chr1:228877939..228879672,2	MCF-7	breast:
4	chr1:228871721..228874007-chr1:228877352..228880161,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 93 )

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs376696944	chr1:228873692-228873693	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs536071971	chr1:228873702-228873703	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs186451021	chr1:228873709-228873710	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs574078596	chr1:228873742-228873743	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs146256177	chr1:228873767-228873768	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs531771641	chr1:228873775-228873776	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs190715673	chr1:228873776-228873777	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs2295255	chr1:228873788-228873789	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs376543517	chr1:228873795-228873796	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs114727738	chr1:228873821-228873822	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs369357572	chr1:228873872-228873873	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs139305562	chr1:228873955-228873956	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs532825585	chr1:228873983-228873984	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs546565407	chr1:228873990-228873991	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs2295256	chr1:228874049-228874050	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Flanking Active TSS Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
16	rs528909267	chr1:228874071-228874072	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs6667487	chr1:228874078-228874079	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Flanking Active TSS Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs34325111	chr1:228874100-228874101	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Flanking Active TSS Enhancers	n/a	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
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
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
abnormal development	18461090	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Melanoma	17363583	CNVD
Myelofibrosis	22110671	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Intellectual disability	21811512	CNVD
Lung adenocarcinoma	21935476	CNVD
early-passage human iPS cells	21368824	CNVD

Chromatin state (count:130 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228870200-228875400	Active TSS	Brain Angular Gyrus	brain
2	chr1:228870400-228873800	Active TSS	Aorta	Aorta
3	chr1:228870400-228873800	Active TSS	Colonic Mucosa	Colon
4	chr1:228870400-228873800	Active TSS	Right Ventricle	heart
5	chr1:228870400-228874000	Active TSS	Brain Anterior Caudate	brain
6	chr1:228870400-228874200	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr1:228870600-228874000	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr1:228870600-228874000	Active TSS	Right Atrium	heart
9	chr1:228870600-228874200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:228870600-228874400	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr1:228870600-228875400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:228870800-228873800	Active TSS	Rectal Smooth Muscle	rectum
13	chr1:228870800-228874000	Active TSS	Fetal Brain Female	brain
14	chr1:228872000-228873800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr1:228872200-228873800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr1:228872400-228875400	Weak transcription	Lung	lung
17	chr1:228872400-228875400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:228872400-228876400	Weak transcription	Hela-S3	cervix
19	chr1:228872400-228880200	Weak transcription	Left Ventricle	heart
20	chr1:228872600-228873800	Active TSS	Thymus	Thymus
21	chr1:228872600-228875400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:228872600-228877800	Weak transcription	Primary T cells from cord blood	blood
23	chr1:228872600-228878400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:228872600-228880600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr1:228872600-228881200	Weak transcription	Esophagus	oesophagus
26	chr1:228872600-228884400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr1:228872800-228873800	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr1:228872800-228874200	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr1:228873000-228873800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:228873000-228873800	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
31	chr1:228873000-228874600	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr1:228873000-228875800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:228873200-228873800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:228873200-228873800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:228873200-228873800	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr1:228873200-228873800	Weak transcription	A549	lung
37	chr1:228873200-228874200	Enhancers	Fetal Brain Male	brain
38	chr1:228873200-228878400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:228873200-228879000	Weak transcription	Ovary	ovary
40	chr1:228873200-228884800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:228873400-228873800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:228873400-228873800	Flanking Active TSS	Fetal Intestine Large	intestine
43	chr1:228873400-228873800	Flanking Active TSS	Fetal Muscle Trunk	muscle
44	chr1:228873400-228873800	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
45	chr1:228873400-228873800	Flanking Active TSS	Psoas Muscle	Psoas
46	chr1:228873400-228874000	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr1:228873400-228874200	Transcr. at gene 5' and 3'	Placenta	Placenta
48	chr1:228873400-228874400	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
49	chr1:228873400-228874600	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:228873400-228876400	Weak transcription	Fetal Kidney	kidney

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