Variant report

Variant	nsv877261
Chromosome Location	chr3:103538656-103716354
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:13)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:103596754..103597389-chr3:103609289..103610010,2	MCF-7	breast:
2	chr3:103709950..103710945-chr3:103925530..103926295,2	MCF-7	breast:
3	chr3:103575079..103576806-chr3:103584240..103586997,2	K562	blood:
4	chr12:57117722..57120174-chr3:103567759..103569281,2	MCF-7	breast:
5	chr3:103575079..103576806-chr3:103584240..103586997,2	K562	blood:
6	chr3:103663959..103665790-chr3:103668581..103671355,2	K562	blood:
7	chr3:103596754..103597389-chr3:103609289..103610010,2	MCF-7	breast:
8	chr3:103672576..103675146-chr3:103946117..103948469,2	K562	blood:
9	chr3:103706366..103707164-chr3:187218063..187218925,2	MCF-7	breast:
10	chr18:59467934..59468577-chr3:103711169..103712107,2	MCF-7	breast:
11	chr3:103663959..103665790-chr3:103668581..103671355,2	K562	blood:
12	chr3:103709966..103710719-chr3:104179327..104180275,3	MCF-7	breast:
13	chr16:12926733..12929305-chr3:103655550..103657071,2	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ALCAM-3	chr3:103646038-103646199	NONHSAT090944
2	lnc-ALCAM-3	chr3:103646039-103646199	XLOC_002744
3	lnc-ALCAM-3	chr3:103689452-103689595	NONHSAT090944

No data

Variant related genes	Relation type
ENSG00000196531	chromatin interactions

Extended variants
information (count: 1718 )
Associated
traits (count: 62 )

Variant overlapped rSNPs/rCNVs (count:1718 , 50 per page) page: 1 2 3 4 5 6 7 ... 35

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1673865	chr3:103538656-103538657	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs578105430	chr3:103538679-103538680	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs552057996	chr3:103538688-103538689	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs570285835	chr3:103538690-103538691	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs112283074	chr3:103538741-103538742	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs560749795	chr3:103538799-103538800	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs552923430	chr3:103538807-103538808	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs189583599	chr3:103538824-103538825	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs78250785	chr3:103538842-103538843	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs75197128	chr3:103538857-103538858	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs548970203	chr3:103538895-103538896	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs546428581	chr3:103538911-103538912	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs149871569	chr3:103538912-103538913	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs181115844	chr3:103538957-103538958	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs185468753	chr3:103539001-103539002	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs559314330	chr3:103539020-103539021	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs577331574	chr3:103539066-103539067	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs189828694	chr3:103539068-103539069	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs951257	chr3:103539120-103539121	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs182001352	chr3:103539220-103539221	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs187124630	chr3:103539229-103539230	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs562898821	chr3:103539249-103539250	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs192137791	chr3:103539279-103539280	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs139918961	chr3:103539307-103539308	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs77663387	chr3:103539316-103539317	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs528401023	chr3:103539344-103539345	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs531395092	chr3:103539411-103539412	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs549602349	chr3:103539413-103539414	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs183519498	chr3:103539479-103539480	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs145336844	chr3:103539519-103539520	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs147701761	chr3:103539532-103539533	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs570038211	chr3:103539642-103539643	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs537457985	chr3:103539650-103539651	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs532841797	chr3:103539703-103539704	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs372679868	chr3:103539766-103539767	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs140783287	chr3:103539772-103539773	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs114437313	chr3:103539773-103539774	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs142416951	chr3:103539778-103539779	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs151288726	chr3:103539780-103539781	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs376802953	chr3:103539802-103539803	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs553492647	chr3:103539841-103539842	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs574939263	chr3:103539850-103539851	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs116570498	chr3:103539891-103539892	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs140612246	chr3:103539983-103539984	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs575032063	chr3:103540025-103540026	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs571368262	chr3:103540040-103540041	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs188511648	chr3:103540086-103540087	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs563970546	chr3:103540133-103540134	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs528375909	chr3:103540165-103540166	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs116076800	chr3:103540382-103540383	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:62)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Renal cell carcinoma	21668985	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	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
Neurodevelopmental disorder	22521361	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	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
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
small cell lung cancer	20016488	CNVD
Ductal carcinoma	22052326	CNVD
Breast cancer	16608533	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Myelofibrosis	22110671	CNVD
Renal cell carcinoma	18765545	CNVD
Breast cancer	21364760	CNVD
Breast cancer	22522925	CNVD
Developmental delay	22180640	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Stenocardia	21860640	CNVD
Vasospasm	21860640	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:103537200-103538800	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr3:103537200-103538800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr3:103537400-103538800	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr3:103537600-103538800	Enhancers	H1 Cell Line	embryonic stem cell
5	chr3:103538200-103539200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr3:103538400-103538800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:103538800-103542800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:103539600-103540000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:103542800-103543400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr3:103556200-103556600	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr3:103556200-103556600	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr3:103564000-103564400	Enhancers	Pancreas	Pancrea
13	chr3:103564600-103564800	Enhancers	HepG2	liver
14	chr3:103564800-103565600	Weak transcription	HepG2	liver
15	chr3:103565600-103567600	Enhancers	HepG2	liver
16	chr3:103576800-103579400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:103577800-103578200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:103580200-103581200	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr3:103580400-103581200	Enhancers	H9 Cell Line	embryonic stem cell
20	chr3:103591400-103591800	Enhancers	Fetal Kidney	kidney
21	chr3:103591800-103592200	Weak transcription	Fetal Kidney	kidney
22	chr3:103592200-103592800	Enhancers	Fetal Kidney	kidney
23	chr3:103592800-103593400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:103604200-103604600	Active TSS	Stomach Smooth Muscle	stomach
25	chr3:103620400-103620600	Enhancers	Pancreas	Pancrea
26	chr3:103620600-103621600	Weak transcription	Pancreas	Pancrea
27	chr3:103621600-103621800	Enhancers	Pancreas	Pancrea
28	chr3:103625800-103626200	Enhancers	HepG2	liver
29	chr3:103637800-103638800	Enhancers	Liver	Liver
30	chr3:103665400-103665800	Enhancers	HepG2	liver
31	chr3:103665800-103666600	Flanking Active TSS	HepG2	liver
32	chr3:103666200-103666600	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr3:103672600-103673200	Enhancers	HepG2	liver
34	chr3:103672800-103673200	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr3:103673200-103679600	Weak transcription	HepG2	liver
36	chr3:103674600-103675000	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr3:103679600-103683600	Enhancers	HepG2	liver
38	chr3:103679800-103680200	Enhancers	Liver	Liver
39	chr3:103681200-103681800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:103681600-103682600	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr3:103682600-103682800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:103684600-103684800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:103684800-103685000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:103685000-103687000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:103694200-103697200	Enhancers	Liver	Liver
46	chr3:103694600-103695400	Enhancers	HepG2	liver
47	chr3:103695400-103696200	Active TSS	HepG2	liver
48	chr3:103695800-103696800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:103696200-103696400	Flanking Active TSS	HepG2	liver
50	chr3:103696200-103697000	Enhancers	Fetal Intestine Small	intestine

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