Variant report

Variant	nsv591890
Chromosome Location	chr3:140776991-140778138
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	chr3:140763223..140765937-chr3:140775586..140778392,2	K562	blood:
2	chr3:140774491..140777455-chr3:140795854..140797381,2	K562	blood:

Variant related genes	Relation type
ENSG00000175093	chromatin interactions

Extended variants
information (count: 28 )
Associated
traits (count: 54 )

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1559896	chr3:140776991-140776992	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs200177153	chr3:140777024-140777025	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs561471789	chr3:140777039-140777040	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs527345826	chr3:140777130-140777131	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs61035025	chr3:140777131-140777132	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs540636910	chr3:140777133-140777134	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs559379913	chr3:140777170-140777171	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs533306607	chr3:140777177-140777178	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs551265734	chr3:140777181-140777182	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs7642476	chr3:140777250-140777251	Weak transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs530740451	chr3:140777266-140777267	Weak transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs150505200	chr3:140777309-140777310	Weak transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs376149371	chr3:140777374-140777375	Weak transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs377688957	chr3:140777426-140777427	Genic enhancers Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs138349104	chr3:140777467-140777468	Genic enhancers Enhancers Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
16	rs553370224	chr3:140777535-140777536	Genic enhancers Enhancers Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
17	rs7645127	chr3:140777575-140777576	Genic enhancers Enhancers Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs539344976	chr3:140777603-140777604	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs557253825	chr3:140777670-140777671	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs575769123	chr3:140777685-140777686	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs373149337	chr3:140777688-140777689	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs542819171	chr3:140777710-140777711	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs371035228	chr3:140777745-140777746	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs189843567	chr3:140777803-140777804	Strong transcription Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs144094245	chr3:140778007-140778008	Strong transcription Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs115448164	chr3:140778035-140778036	Strong transcription Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs536110925	chr3:140778120-140778121	Strong transcription Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs147313616	chr3:140778126-140778127	Strong transcription Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:54)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
microdeletion syndrome	22180640	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
Colorectal cancer	18645599	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Hepatocellular carcinoma	16750200	CNVD
Lung cancer	16740712	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Blepharophimosis-ptosis-epicanthus inversus syndrome	22067867	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
abnormal development	18461090	CNVD
Schizophrenia	17989066	CNVD
Cancer	21129771	CNVD
Ovarian cancer	23621864	CNVD
Congenital anomalies of the kidney and urinary tract	20605837	CNVD
Breast cancer	22522925	CNVD
Cancer	20164919	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140772000-140779000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:140772000-140782600	Weak transcription	Psoas Muscle	Psoas
3	chr3:140772200-140777400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:140772200-140777600	Enhancers	Fetal Heart	heart
5	chr3:140772200-140779000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:140774000-140777600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:140774000-140777600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr3:140774000-140777600	Enhancers	Brain Germinal Matrix	brain
9	chr3:140774400-140777000	Enhancers	Left Ventricle	heart
10	chr3:140774400-140777200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:140774600-140777400	Enhancers	Fetal Kidney	kidney
12	chr3:140774600-140777800	Enhancers	Right Ventricle	heart
13	chr3:140775000-140777400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:140775200-140779000	Weak transcription	Fetal Lung	lung
15	chr3:140775400-140777000	Enhancers	Fetal Brain Male	brain
16	chr3:140775800-140777400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:140775800-140777400	Enhancers	Fetal Brain Female	brain
18	chr3:140775800-140777400	Weak transcription	Dnd41	blood
19	chr3:140775800-140777600	Enhancers	Fetal Muscle Trunk	muscle
20	chr3:140775800-140784200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:140776000-140777400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:140776000-140777800	Weak transcription	Fetal Stomach	stomach
23	chr3:140776000-140779600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:140776000-140783400	Weak transcription	Right Atrium	heart
25	chr3:140776000-140787600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr3:140776400-140777200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:140776400-140779000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:140776600-140777000	Enhancers	Placenta	Placenta
29	chr3:140776600-140779200	Enhancers	Pancreas	Pancrea
30	chr3:140776600-140787200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:140776800-140777000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:140776800-140777600	Genic enhancers	Fetal Muscle Leg	muscle
33	chr3:140777000-140777400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:140777200-140778000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:140777200-140781200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:140777400-140777800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:140777400-140778000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr3:140777400-140778000	ZNF genes & repeats	Dnd41	blood
39	chr3:140777400-140778400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:140777400-140779000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:140777400-140782600	Weak transcription	Fetal Kidney	kidney
42	chr3:140777400-140795000	Weak transcription	Fetal Brain Female	brain
43	chr3:140777600-140777800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:140777600-140778000	Strong transcription	Fetal Muscle Leg	muscle
45	chr3:140777600-140778600	Weak transcription	Fetal Heart	heart
46	chr3:140777600-140782800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr3:140777600-140785200	Weak transcription	Brain Germinal Matrix	brain
48	chr3:140777600-140789600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:140777800-140778400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
50	chr3:140777800-140778400	ZNF genes & repeats	Fetal Stomach	stomach

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