Variant report

Variant	nsv613913
Chromosome Location	chr9:25548319-25621151
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:25612676..25613650-chr9:25715920..25716890,2	MCF-7	breast:
2	chr9:25600112..25602415-chr9:25676030..25679232,3	MCF-7	breast:
3	chr9:25599854..25601775-chr9:97221816..97224638,2	MCF-7	breast:
4	chr9:25613138..25615070-chr9:25677040..25679432,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IFT74-4	chr9:25617639-25617675	XLOC_007305
2	lnc-IFT74-4	chr9:25613547-25613770	XLOC_007305

Variant related genes	Relation type
ENSG00000198680	chromatin interactions

Extended variants
information (count: 1617 )
Associated
traits (count: 130 )

Variant overlapped rSNPs/rCNVs (count:1617 , 50 per page) page: 1 2 3 4 5 6 7 ... 33

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs150143266	chr9:25549415-25549416	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs545032311	chr9:25549470-25549471	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs563440889	chr9:25549504-25549505	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs575692387	chr9:25549523-25549524	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs543158581	chr9:25549534-25549535	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs564484844	chr9:25549584-25549585	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs531770656	chr9:25549588-25549589	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs528746482	chr9:25549627-25549628	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs113275917	chr9:25549688-25549689	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs547295827	chr9:25549770-25549771	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs550175277	chr9:25549774-25549775	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs541948503	chr9:25549788-25549789	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs60463530	chr9:25549806-25549807	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs56691581	chr9:25549833-25549834	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs543622999	chr9:25549836-25549837	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs563373389	chr9:25549855-25549856	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs4977994	chr9:25549903-25549904	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs536752236	chr9:25549950-25549951	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs563486964	chr9:25549969-25549970	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs549133566	chr9:25549976-25549977	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs567366149	chr9:25549988-25549989	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs575209325	chr9:25550074-25550075	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs534853409	chr9:25550115-25550116	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs552830227	chr9:25550156-25550157	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs577564850	chr9:25550266-25550267	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs12004929	chr9:25550283-25550284	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs12004906	chr9:25550290-25550291	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs564153576	chr9:25550310-25550311	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs1412379	chr9:25550324-25550325	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs1412380	chr9:25550340-25550341	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs369582892	chr9:25550366-25550367	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs573335240	chr9:25550368-25550369	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs182394295	chr9:25550379-25550380	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs187327913	chr9:25550387-25550388	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs532864073	chr9:25550395-25550396	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs143651383	chr9:25550412-25550413	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs190889768	chr9:25550434-25550435	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs374589701	chr9:25550435-25550436	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs138250807	chr9:25550447-25550448	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs7023485	chr9:25550454-25550455	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs567385343	chr9:25550519-25550520	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs528270999	chr9:25550570-25550571	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs546431382	chr9:25550571-25550572	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs373808388	chr9:25550572-25550573	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs73479856	chr9:25550590-25550591	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs367859115	chr9:25553618-25553619	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs112917457	chr9:25553633-25553634	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs551730093	chr9:25553667-25553668	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs555451519	chr9:25553690-25553691	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs563967396	chr9:25553693-25553694	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:130)

Disease	PMID	Source
Breast cancer	16608533	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	16272173	CNVD
Medulloblastoma	21979893	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17133270	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Cervical cancer	21063398	CNVD
Retinoblastoma	22278416	CNVD
Splenic marginal zone lymphoma	18492102	CNVD
Melanoma	18172304	CNVD
Biliary cancer	19435499	CNVD
Gastric cancer	21586687	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myopathy	18421352	CNVD
Neuroblastoma	18664255	CNVD
Acute lymphoblastic leukemia	18957548	CNVD
Myeloproliferative neoplasm	17564968	CNVD
Malignant meningioma	17937814	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	17603634	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Oligodendroglial tumors	17285580	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
microdeletion syndrome	16199537	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Cancer	20164919	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Lung cancer	18438408	CNVD
Urothelial carcinoma	21177765	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic myeloid leukemia	21384125	CNVD
Breast cancer	21785460	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Renal cell carcinoma	21668985	CNVD
Myelodysplastic syndrome	21251322	CNVD
Autism	22495311	CNVD
Hepatocellular carcinoma	18803288	CNVD
Metanephric adenoma	20802469	CNVD
Developmental delay	21147756	CNVD
Pilocytic astrocytoma	18670637	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Melanoma	22183965	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Non-small cell lung cancer	19010865	CNVD
Myoepithelioma	18604193	CNVD
Cancer	22183965	CNVD
Glioma	17123091	CNVD
Mental retardation	17124404	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Acute lymphoblastic leukemia	18768390	CNVD
Leukemia	19602459	CNVD
Acute monocytic leukemia	16498392	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Leukemia	18688285	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Acute myeloid leukemia	19651601	CNVD
Coronary Disease	20032323	CNVD
Squamous cell cancer	20885788	CNVD
Hirschsprung''s Disease	21712996	CNVD
Cancer	21732550	CNVD
Gastric cancer	22539939	CNVD
Cancer	21183584	CNVD
T-cell lymphomas	19863542	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Metastatic melanoma	18483359	CNVD
Non-small cell lung cancer	20864512	CNVD
Cervical cancer	21062161	CNVD
Acute myeloid leukemia	16864856	CNVD
Glioblastoma	17090523	CNVD
Lung cancer	16773561	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Colorectal cancer	16774939	CNVD
Bladder cancer	19088036	CNVD
Colorectal cancer	16272173	CNVD
Melanoma	16977458	CNVD
Glioblastoma multiforme	17369134	CNVD
Chagasic megaesophagus	20163722	CNVD
Melanoma	19566914	CNVD
Squamous cell cancer	19047905	CNVD
Lung adenocarcinoma	19525976	CNVD
Lung cancer	19525976	CNVD
Hodgkin''s lymphoma	18179710	CNVD
Adenoid cystic carcinoma	18332873	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Acute myeloid leukemia	21251322	CNVD
Oral cancer	21386901	CNVD
Breast cancer	21858162	CNVD
Breast cancer	21364760	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Pancreatic cancer	21811587	CNVD
Bipolar disorder	19114987	CNVD
Barrett''s syndrome	19417022	CNVD
Non-small cell lung cancer	16651412	CNVD
Myelofibrosis	22110671	CNVD
Urothelial cell carcinoma	18451213	CNVD
polycythaemia	22829968	CNVD
Neuroblastoma	21899760	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:25549400-25549600	Enhancers	Pancreatic Islets	Pancreatic Islet
2	chr9:25549400-25550600	Enhancers	Fetal Heart	heart
3	chr9:25553600-25554600	Enhancers	Placenta Amnion	Placenta Amnion
4	chr9:25554600-25555400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr9:25555400-25555800	Enhancers	Placenta Amnion	Placenta Amnion
6	chr9:25555800-25556000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr9:25556000-25558000	Enhancers	Placenta Amnion	Placenta Amnion
8	chr9:25557400-25558800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:25561800-25562800	Enhancers	Placenta	Placenta
10	chr9:25562000-25562200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:25562200-25562600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:25562400-25563600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:25562800-25563600	Weak transcription	Placenta	Placenta
14	chr9:25563600-25563800	Enhancers	Placenta	Placenta
15	chr9:25563600-25564000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:25570800-25571200	Enhancers	Fetal Brain Female	brain
17	chr9:25570800-25571200	Enhancers	Placenta Amnion	Placenta Amnion
18	chr9:25571000-25571400	Active TSS	Fetal Brain Male	brain
19	chr9:25576200-25577600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:25576800-25577400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr9:25577400-25578600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr9:25577600-25583000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr9:25581800-25583000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:25583000-25584000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr9:25583000-25584600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr9:25584600-25585000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr9:25585000-25585800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:25585200-25585600	Active TSS	Psoas Muscle	Psoas
29	chr9:25585800-25590400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr9:25590400-25591000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:25599200-25599800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr9:25599400-25599800	Enhancers	Fetal Lung	lung
33	chr9:25601000-25602400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr9:25601200-25602400	Enhancers	Colon Smooth Muscle	Colon
35	chr9:25601800-25603400	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr9:25601800-25603800	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr9:25601800-25604000	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr9:25602000-25603400	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr9:25602000-25603800	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr9:25602200-25602400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr9:25602200-25602600	Enhancers	Fetal Intestine Small	intestine
42	chr9:25602200-25602800	Enhancers	Placenta Amnion	Placenta Amnion
43	chr9:25602200-25603000	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr9:25602200-25603400	Enhancers	H1 Cell Line	embryonic stem cell
45	chr9:25602200-25603400	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr9:25602200-25603400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr9:25602200-25603600	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr9:25602200-25604400	Enhancers	Stomach Mucosa	stomach
49	chr9:25602400-25602600	Enhancers	Gastric	stomach
50	chr9:25602400-25603400	Enhancers	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links