Variant report

Variant	nsv613599
Chromosome Location	chr9:12206873-12342809
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:376)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:376 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr9:12328968-12329168	HepG2	liver:	n/a	n/a
2	BACH1	chr9:12292536-12292567	H1-hESC	embryonic stem cell:	n/a	n/a
3	BATF	chr9:12329455-12329670	GM12878	blood:	n/a	n/a
4	BATF	chr9:12230772-12231081	GM12878	blood:	n/a	n/a
5	BCLAF1	chr9:12329426-12329668	GM12878	blood:	n/a	n/a
6	BHLHE40	chr9:12328995-12329158	K562	blood:	n/a	n/a
7	BHLHE40	chr9:12329021-12329257	GM12878	blood:	n/a	n/a
8	BHLHE40	chr9:12328884-12329725	HepG2	liver:	n/a	n/a
9	CEBPB	chr9:12208833-12209071	HepG2	liver:	n/a	chr9:12208898-12208909 chr9:12208899-12208908 chr9:12208897-12208910
10	CEBPB	chr9:12288039-12288167	HepG2	liver:	n/a	n/a
11	CHD1	chr9:12314638-12314797	GM12878	blood:	n/a	n/a
12	CHD2	chr9:12314733-12314838	GM12878	blood:	n/a	n/a
13	CHD2	chr9:12319226-12319370	GM12878	blood:	n/a	n/a
14	CTCF	chr9:12215488-12215552	GM13977	blood:	n/a	n/a
15	CTCF	chr9:12329367-12329706	K562	blood:	n/a	n/a
16	CTCF	chr9:12329449-12329693	GM19239	blood:	n/a	n/a
17	CTCF	chr9:12329500-12329650	AG04450	lung:	n/a	n/a
18	CTCF	chr9:12329500-12329650	WERI-Rb-1	eye:	n/a	n/a
19	CTCF	chr9:12329460-12329610	A549	lung:	n/a	n/a
20	CTCF	chr9:12329500-12329650	BJ	skin:	n/a	n/a
21	CTCF	chr9:12329403-12329717	GM19238	blood:	n/a	n/a
22	CTCF	chr9:12329520-12329670	GM12868	blood:	n/a	n/a
23	CTCF	chr9:12329466-12329689	Hela-S3	cervix:	n/a	n/a
24	CTCF	chr9:12329436-12329697	Pancreas_OC	pancreas:	n/a	n/a
25	CTCF	chr9:12329500-12329650	SAEC	small airway:	n/a	n/a
26	CTCF	chr9:12329480-12329630	AG09319	gingival:	n/a	n/a
27	CTCF	chr9:12329464-12329699	HepG2	liver:	n/a	n/a
28	CTCF	chr9:12329120-12329270	GM12866	blood:	n/a	n/a
29	CTCF	chr9:12325673-12325794	GM20000	blood:	n/a	n/a
30	CTCF	chr9:12329322-12329716	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr9:12328860-12329010	HepG2	liver:	n/a	n/a
32	CTCF	chr9:12329368-12329671	K562	blood:	n/a	n/a
33	CTCF	chr9:12329420-12329570	HMEC	breast:	n/a	n/a
34	CTCF	chr9:12329460-12329610	BE2_C	brain:	n/a	n/a
35	CTCF	chr9:12329460-12329610	HCT-116	colon:	n/a	n/a
36	CTCF	chr9:12329407-12329722	Gliobla	brain:	n/a	n/a
37	CTCF	chr9:12329400-12329550	HFF-Myc	foreskin:	n/a	n/a
38	CTCF	chr9:12329500-12329650	GM06990	blood:	n/a	n/a
39	CTCF	chr9:12230966-12231007	Kidney_OC	kidney:	n/a	n/a
40	CTCF	chr9:12329500-12329650	GM12873	blood:	n/a	n/a
41	CTCF	chr9:12329520-12329670	HFF-Myc	foreskin:	n/a	n/a
42	CTCF	chr9:12329263-12329335	GM19238	blood:	n/a	n/a
43	CTCF	chr9:12329180-12329330	HRE	kidney:	n/a	n/a
44	CTCF	chr9:12329330-12329693	T-47D	breast:	n/a	n/a
45	CTCF	chr9:12329421-12329698	ProgFib	skin:	n/a	n/a
46	CTCF	chr9:12210677-12210803	Kidney_OC	kidney:	n/a	n/a
47	CTCF	chr9:12329160-12329310	AG04450	lung:	n/a	n/a
48	CTCF	chr9:12329390-12329658	A549	lung:	n/a	n/a
49	CTCF	chr9:12329460-12329610	HAc	cerebellar:	n/a	n/a
50	CTCF	chr9:12329500-12329650	AoAF	blood vessel:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:10365979..10366914-chr9:12329143..12329893,2	MCF-7	breast:
2	chr9:12268631..12271178-chr9:12273434..12276211,2	K562	blood:
3	chr9:10855828..10856443-chr9:12329128..12329639,2	MCF-7	breast:
4	chr16:89002000..89004763-chr9:12244429..12246932,2	MCF-7	breast:
5	chr9:12268631..12271178-chr9:12273434..12276211,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TYRP1-4	chr9:12287320-12288238	NONHSAT130222

No data

Variant related genes	Relation type
ENSG00000231491	TF binding region
RNU2-47P	TF binding region
ENSG00000261226	chromatin interactions

Extended variants
information (count: 1973 )
Associated
traits (count: 105 )

Variant overlapped rSNPs/rCNVs (count:1973 , 50 per page) page: 1 2 3 4 5 6 7 ... 40

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs543359453	chr9:12212616-12212617	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs565239580	chr9:12212622-12212623	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs575147048	chr9:12212634-12212635	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs543849601	chr9:12212635-12212636	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs560967689	chr9:12212636-12212637	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs375762420	chr9:12212638-12212639	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs112454203	chr9:12212640-12212641	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs546758217	chr9:12212651-12212652	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs560351782	chr9:12212677-12212678	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs7031136	chr9:12212697-12212698	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs552473940	chr9:12212704-12212705	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs569075023	chr9:12212711-12212712	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs540051058	chr9:12212712-12212713	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs538173726	chr9:12212737-12212738	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs75966373	chr9:12212751-12212752	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs184720528	chr9:12212768-12212769	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs149093849	chr9:12212778-12212779	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs553059900	chr9:12212790-12212791	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs534673214	chr9:12212799-12212800	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs538868272	chr9:12212807-12212808	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs142164631	chr9:12212816-12212817	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs189024815	chr9:12212821-12212822	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs376430736	chr9:12212825-12212826	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs560713542	chr9:12212890-12212891	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs111377781	chr9:12212906-12212907	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs7859262	chr9:12212956-12212957	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs191982026	chr9:12212958-12212959	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs185692122	chr9:12213012-12213013	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs532313372	chr9:12213036-12213037	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs552382936	chr9:12213038-12213039	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs10960529	chr9:12213047-12213048	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs531501324	chr9:12213111-12213112	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs562202495	chr9:12213113-12213114	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs548501361	chr9:12213133-12213134	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs4442242	chr9:12213134-12213135	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs140996227	chr9:12213138-12213139	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs4521852	chr9:12213147-12213148	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs190265597	chr9:12213159-12213160	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs558882663	chr9:12213163-12213164	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs56258012	chr9:12213165-12213166	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs539756433	chr9:12213195-12213196	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs549732628	chr9:12213216-12213217	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs7848763	chr9:12213224-12213225	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs180965945	chr9:12213229-12213230	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs540251385	chr9:12213230-12213231	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs555122095	chr9:12213251-12213252	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs568544164	chr9:12213312-12213313	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs185886741	chr9:12213341-12213342	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs117111122	chr9:12213361-12213362	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs541711494	chr9:12213363-12213364	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:105)

Disease	PMID	Source
Disorders of sex development	21048976	CNVD
Honadal dysgenesis	21048976	CNVD
Medulloblastoma	21979893	CNVD
Lung cancer	16740712	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
abnormal development	18461090	CNVD
Glioblastoma multiforme	21080181	CNVD
Breast cancer	16608533	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	16272173	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
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
Pleomorphic xanthoastrocytoma	20730472	CNVD
microdeletion syndrome	16199537	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Cancer	20164919	CNVD
Chronic myeloid leukemia	21384125	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
Oral cancer	21386901	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	21785460	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21858162	CNVD
Renal cell carcinoma	21668985	CNVD
Myelodysplastic syndrome	21251322	CNVD
Autism	22495311	CNVD
Hepatocellular carcinoma	18803288	CNVD
Breast cancer	21364760	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma	19074898	CNVD
Malignant melanoma	19074898	CNVD
Prostate cancer	16573809	CNVD
Metanephric adenoma	20802469	CNVD
Cancer	20164920	CNVD
Developmental delay	21147756	CNVD
small cell lung cancer	21764851	CNVD
Glioblastoma multiforme	22286061	CNVD
Glioma	17123091	CNVD
Lung cancer	16773561	CNVD
Colorectal cancer	16272173	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Gastric cancer	16891809	CNVD
Mental retardation	17847001	CNVD
Cutaneous squamous cell carcinomas	17420988	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Pilocytic astrocytoma	18670637	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Acute myeloid leukemia	21251322	CNVD
Breast cancer	21611746	CNVD
Melanoma	22183965	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Autism	20858261	CNVD
Epilepsy	20858261	CNVD
Mental retardation	20858261	CNVD

Chromatin state (count:134 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12212600-12213000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr9:12212600-12213600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:12212800-12214000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:12213000-12213400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:12213000-12213800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr9:12213400-12214200	Enhancers	Brain Germinal Matrix	brain
7	chr9:12213400-12214400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:12213800-12214200	Enhancers	Brain Hippocampus Middle	brain
9	chr9:12221800-12222000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr9:12222000-12224400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr9:12224200-12224600	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr9:12224200-12225000	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr9:12224200-12225000	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr9:12224400-12224800	Enhancers	H9 Cell Line	embryonic stem cell
15	chr9:12224400-12224800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:12231000-12231400	Enhancers	Liver	Liver
17	chr9:12231200-12231600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:12231400-12233400	Weak transcription	Liver	Liver
19	chr9:12231600-12232000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:12233400-12233800	Enhancers	Liver	Liver
21	chr9:12235200-12235600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr9:12241200-12242000	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr9:12241400-12243200	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr9:12241600-12242000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr9:12241600-12242000	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr9:12241600-12242000	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr9:12241600-12242000	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr9:12241600-12242000	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr9:12242600-12242800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
30	chr9:12260800-12261200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr9:12271200-12271600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr9:12271200-12274800	Enhancers	Rectal Smooth Muscle	rectum
33	chr9:12271200-12275200	Enhancers	Fetal Brain Male	brain
34	chr9:12271400-12271600	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr9:12271400-12272000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr9:12271400-12273400	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr9:12271600-12272000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr9:12271600-12272000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr9:12271600-12272600	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr9:12271600-12272800	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr9:12271600-12274400	Enhancers	Colon Smooth Muscle	Colon
42	chr9:12271600-12276600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr9:12271600-12277600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:12272000-12272400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr9:12272000-12273000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr9:12272400-12272800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr9:12272400-12273000	Enhancers	Brain Cingulate Gyrus	brain
48	chr9:12272400-12273400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr9:12272400-12274000	Enhancers	Fetal Stomach	stomach
50	chr9:12272600-12272800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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