Variant report

Variant	esv3492871
Chromosome Location	chr1:246935621-246936002
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:246935717-246935734	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:246935763-246935774	Gliobla	brain:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:246933982..246937125-chr1:246938877..246940973,4	K562	blood:
2	chr1:246935414..246937125-chr1:246938877..246940791,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCCPDH-1	chr1:246935607-246937461	NONHSAT010724
2	lnc-SCCPDH-1	chr1:246935603-246939074	ENSG00000260855.1

No data

Variant related genes	Relation type
ENSG00000227953	TF binding region
ENSG00000227953	chromatin interactions

Extended variants
information (count: 17 )
Associated
traits (count: 84 )

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	rs148091883	chr1:246935627-246935628	Weak transcription Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs374505183	chr1:246935710-246935711	Weak transcription Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs12403128	chr1:246935739-246935740	Weak transcription Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
4	rs563256780	chr1:246935748-246935749	Weak transcription Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs547038614	chr1:246935753-246935754	Weak transcription Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs186599550	chr1:246935754-246935755	Weak transcription Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs538970009	chr1:246935765-246935766	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
8	rs558452308	chr1:246935816-246935817	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs569080975	chr1:246935830-246935831	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
10	rs369811769	chr1:246935840-246935841	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs537536486	chr1:246935842-246935843	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
12	rs554611553	chr1:246935870-246935871	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
13	rs111333114	chr1:246935888-246935889	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
14	rs114238653	chr1:246935910-246935911	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
15	rs553370350	chr1:246935931-246935932	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
16	rs372665443	chr1:246935940-246935941	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
17	rs375642430	chr1:246935960-246935961	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:84)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Melanoma	18172304	CNVD
Medulloblastoma	21979893	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
Neuroblastoma	21899760	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Acute myeloid leukemia	20729466	CNVD
Testicular germ cell tumor	18059402	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Lung cancer	18438408	CNVD
Medulloblastoma	16783165	CNVD
Basal cell lymphoma	17170743	CNVD
Basal cell lymphoma	17053054	CNVD
Congenital abnormalities	21549014	CNVD
Developmental delay	21549014	CNVD
Mental retardation	21549014	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Cancer	17060936	CNVD
abnormal development	18461090	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Non-small cell lung cancer	21829676	CNVD
Multiple myeloma	16616336	CNVD
Ovarian cancer	21720365	CNVD
Glioblastoma multiforme	22291905	CNVD
Myelofibrosis	22110671	CNVD
Disease	21936942	CNVD
laryngomalacia	21936942	CNVD
GLUT3 deficiency syndrome	20509907	CNVD
Developmental delay	21373258	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Developmental delay	19490664	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Cutaneous malignant melanoma	18794153	CNVD
Astrocytoma	17934521	CNVD
Neurocytoma	17123091	CNVD
Central neurocytomas	17123091	CNVD
Breast cancer	20409316	CNVD
Fibroblasts	17951408	CNVD
Lung cancer	17951408	CNVD
Stenocardia	21860640	CNVD
Vasospasm	21860640	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246888400-246946400	Weak transcription	Small Intestine	intestine
2	chr1:246888600-246945600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:246895000-246942200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:246895400-246938600	Weak transcription	Fetal Heart	heart
5	chr1:246902800-246952800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:246904600-246942800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:246905000-246945800	Weak transcription	Psoas Muscle	Psoas
8	chr1:246917600-246936000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr1:246920800-246944200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:246921200-246943200	Strong transcription	Dnd41	blood
11	chr1:246921600-246945800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:246922000-246936400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:246922200-246936000	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr1:246922200-246936000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:246922200-246936200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:246922200-246937000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr1:246922200-246944600	Strong transcription	Fetal Muscle Trunk	muscle
18	chr1:246922600-246936400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:246923000-246936200	Strong transcription	Primary hematopoietic stem cells	blood
20	chr1:246923200-246945000	Strong transcription	Fetal Muscle Leg	muscle
21	chr1:246924000-246941200	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr1:246924000-246944200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr1:246924400-246939200	Weak transcription	Colonic Mucosa	Colon
24	chr1:246924400-246945800	Weak transcription	Primary B cells from cord blood	blood
25	chr1:246925200-246952200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:246925400-246936600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:246926400-246939200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:246928600-246937000	Strong transcription	Fetal Stomach	stomach
29	chr1:246928800-246944800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:246929200-246936800	Strong transcription	Fetal Brain Female	brain
31	chr1:246930600-246939000	Weak transcription	Thymus	Thymus
32	chr1:246931000-246936800	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr1:246931200-246937800	Weak transcription	NH-A	brain
34	chr1:246931200-246940600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:246932000-246936600	Weak transcription	Aorta	Aorta
36	chr1:246932000-246939200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:246932400-246939000	Weak transcription	Pancreas	Pancrea
38	chr1:246932400-246945800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:246932400-246952000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:246932600-246938600	Weak transcription	Brain Substantia Nigra	brain
41	chr1:246932600-246939200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:246932600-246939400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:246932600-246948000	Strong transcription	Liver	Liver
44	chr1:246932600-246948600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:246932600-246948600	Weak transcription	Esophagus	oesophagus
46	chr1:246932800-246936600	Weak transcription	NHEK	skin
47	chr1:246932800-246937800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:246932800-246938400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:246932800-246938600	Weak transcription	HUVEC	blood vessel
50	chr1:246932800-246938600	Weak transcription	Osteobl	bone

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