Variant report

Variant	nsv460868
Chromosome Location	chr3:140124599-140169657
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:7)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:140160036..140161866-chr3:140164735..140166930,2	K562	blood:
2	chr3:140158384..140160631-chr3:140165568..140168187,2	MCF-7	breast:
3	chr3:140111455..140114445-chr3:140122370..140124734,2	MCF-7	breast:
4	chr3:140161141..140164298-chr3:140170200..140174173,3	MCF-7	breast:
5	chr3:140153110..140155513-chr3:140157177..140159656,3	K562	blood:
6	chr3:140153110..140155513-chr3:140157177..140159656,3	K562	blood:
7	chr3:140145580..140147650-chr3:140148018..140150573,2	MCF-7	breast:
8	chr3:140160036..140161866-chr3:140164735..140166930,2	K562	blood:
9	chr3:140158384..140160631-chr3:140165568..140168187,2	MCF-7	breast:
10	chr3:140145580..140147650-chr3:140148018..140150573,2	MCF-7	breast:
11	chr3:140105349..140107747-chr3:140133928..140135787,2	K562	blood:

(count:7 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NMNAT3-3	chr3:140168277-140168618	ENSG00000249290.1
2	lnc-NMNAT3-9	chr3:140145498-140145552	ucscGeneNc_uc003esv_1
3	lnc-NMNAT3-9	chr3:140143916-140144150	ucscGeneNc_uc003esv_1
4	lnc-NMNAT3-9	chr3:140136721-140139968	ucscGeneNc_uc003esv_1
5	lnc-NMNAT3-3	chr3:140168352-140168618	ENSG00000249290.1
6	lnc-NMNAT3-3	chr3:140168784-140168885	ENSG00000249290.1
7	lnc-NMNAT3-3	chr3:140168784-140168885	ENSG00000249290.1

No data

Variant related genes	Relation type
ENSG00000249290	chromatin interactions

Extended variants
information (count: 1931 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:1931 , 50 per page) page: 1 2 3 4 5 6 7 ... 39

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs10513111	chr3:140124599-140124600	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs182404776	chr3:140124602-140124603	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs573048504	chr3:140124608-140124609	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs10513112	chr3:140124616-140124617	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
5	rs11706731	chr3:140124629-140124630	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs576808200	chr3:140124708-140124709	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs544325690	chr3:140124780-140124781	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs6790656	chr3:140124787-140124788	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs13084893	chr3:140124801-140124802	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs548721643	chr3:140124807-140124808	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs34368982	chr3:140124854-140124855	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs145153426	chr3:140124884-140124885	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs528035674	chr3:140124904-140124905	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs552584753	chr3:140124972-140124973	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs11713238	chr3:140124982-140124983	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs11713247	chr3:140125018-140125019	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs142309205	chr3:140125025-140125026	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs370215689	chr3:140125033-140125034	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs116696652	chr3:140125037-140125038	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs561491969	chr3:140125091-140125092	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs187887373	chr3:140125106-140125107	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs568934121	chr3:140125113-140125114	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs146140134	chr3:140125135-140125136	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs554797948	chr3:140125149-140125150	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs11415454	chr3:140125203-140125204	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs543975080	chr3:140125217-140125218	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs191071158	chr3:140125237-140125238	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs532355929	chr3:140125318-140125319	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs13100720	chr3:140125394-140125395	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs558547497	chr3:140125412-140125413	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs576847237	chr3:140125499-140125500	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs79402248	chr3:140125564-140125565	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs367989365	chr3:140125603-140125604	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs182583412	chr3:140125671-140125672	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs147830991	chr3:140125701-140125702	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs993483	chr3:140125714-140125715	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs141315485	chr3:140125721-140125722	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs143533508	chr3:140125738-140125739	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs547967714	chr3:140125741-140125742	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs546498259	chr3:140125762-140125763	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs564736269	chr3:140125773-140125774	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs567957915	chr3:140125774-140125775	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs532155513	chr3:140125791-140125792	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs550549843	chr3:140125793-140125794	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs370168004	chr3:140125806-140125807	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs568869973	chr3:140125838-140125839	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs529839702	chr3:140125895-140125896	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs536748700	chr3:140125904-140125905	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs148013909	chr3:140125922-140125923	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs566684167	chr3:140125927-140125928	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:59)

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
Cancer	21129771	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
Multiple myeloma	17550852	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
Myelofibrosis	22110671	CNVD
abnormal development	18461090	CNVD
Dyslexia	22102821	CNVD
Congenital anomalies of the kidney and urinary tract	20605837	CNVD
Cancer	20164919	CNVD
Blepharophimosis syndrome	18726931	CNVD
Blepharophimosis syndrome	18642388	CNVD
Disorders of sex development	22290220	CNVD
Non-syndromic sensorineural hearing loss	19491894	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:291 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140119200-140124800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:140121000-140127800	Weak transcription	Adipose Nuclei	Adipose
3	chr3:140123000-140124800	Strong transcription	HSMMtube	muscle
4	chr3:140123000-140128200	Strong transcription	Ovary	ovary
5	chr3:140123600-140127200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:140123800-140127600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:140124400-140126800	Enhancers	HMEC	breast
8	chr3:140124800-140125200	Genic enhancers	HSMMtube	muscle
9	chr3:140124800-140126200	Enhancers	NHEK	skin
10	chr3:140124800-140126400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr3:140124800-140126400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:140124800-140126400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:140124800-140126400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:140125000-140125200	Enhancers	Right Atrium	heart
15	chr3:140125200-140127800	Weak transcription	HSMMtube	muscle
16	chr3:140125200-140128000	Weak transcription	Right Atrium	heart
17	chr3:140126200-140126400	Enhancers	Pancreas	Pancrea
18	chr3:140126400-140126800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:140126400-140127800	Weak transcription	Pancreas	Pancrea
20	chr3:140126800-140127200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:140127200-140127800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:140127600-140127800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:140127800-140128000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:140127800-140128200	ZNF genes & repeats	Adipose Nuclei	Adipose
25	chr3:140127800-140128200	Enhancers	Pancreas	Pancrea
26	chr3:140127800-140128400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:140127800-140128400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:140127800-140128600	Strong transcription	HSMMtube	muscle
29	chr3:140128000-140128400	ZNF genes & repeats	Right Atrium	heart
30	chr3:140128000-140131800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:140128200-140139600	Weak transcription	Ovary	ovary
32	chr3:140128400-140130800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:140128400-140139600	Weak transcription	Right Atrium	heart
34	chr3:140128600-140130400	Weak transcription	HSMMtube	muscle
35	chr3:140130400-140130800	Strong transcription	HSMMtube	muscle
36	chr3:140130800-140131400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:140130800-140134600	Weak transcription	HSMMtube	muscle
38	chr3:140131400-140139600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:140134600-140134800	Strong transcription	HSMMtube	muscle
40	chr3:140134800-140139400	Weak transcription	HSMMtube	muscle
41	chr3:140135200-140136400	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr3:140135400-140135800	Enhancers	Pancreas	Pancrea
43	chr3:140135400-140136200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:140135600-140136000	Enhancers	Brain Substantia Nigra	brain
45	chr3:140135600-140137200	Enhancers	Liver	Liver
46	chr3:140135800-140136400	Enhancers	Brain Germinal Matrix	brain
47	chr3:140135800-140139800	Weak transcription	Pancreas	Pancrea
48	chr3:140136400-140139400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:140138800-140143600	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr3:140139000-140139200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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