Variant report

Variant	nsv1038241
Chromosome Location	chr9:104943675-105046156
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:150)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:19)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:150 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr9:104949932-104950119	HepG2	liver:	n/a	n/a
2	CEBPB	chr9:104986298-104986457	H1-hESC	embryonic stem cell:	n/a	n/a
3	CEBPB	chr9:105045628-105045943	HepG2	liver:	n/a	n/a
4	CEBPB	chr9:105045700-105045900	A549	lung:	n/a	n/a
5	CEBPB	chr9:105015369-105015524	H1-hESC	embryonic stem cell:	n/a	n/a
6	CEBPB	chr9:104999513-104999769	HepG2	liver:	n/a	chr9:104999628-104999639
7	CTCF	chr9:105015517-105015635	MCF-7	breast:	n/a	chr9:105015565-105015573
8	CTCF	chr9:104948460-104948610	HRPEpiC	eye:	n/a	n/a
9	CTCF	chr9:105015506-105015634	MCF-7	breast:	n/a	chr9:105015565-105015573
10	CTCF	chr9:105015460-105015610	HEK293	kidney:	n/a	chr9:105015565-105015573
11	CTCF	chr9:105015560-105015710	WERI-Rb-1	eye:	n/a	chr9:105015565-105015573
12	CTCF	chr9:104982658-104982752	GM13976	blood:	n/a	n/a
13	CTCF	chr9:105015420-105015570	Caco-2	colon:	n/a	n/a
14	CTCF	chr9:105019456-105019525	GM13976	blood:	n/a	n/a
15	CTCF	chr9:105015420-105015729	H1-hESC	embryonic stem cell:	n/a	chr9:105015565-105015573
16	CTCF	chr9:105017180-105017330	GM12866	blood:	n/a	n/a
17	CTCF	chr9:105039793-105039858	Kidney_OC	kidney:	n/a	n/a
18	CTCF	chr9:104997625-104997683	Fibrobl	skin:	n/a	n/a
19	CTCF	chr9:104948440-104948590	MCF-7	breast:	n/a	n/a
20	CTCF	chr9:105015408-105015699	H1-hESC	embryonic stem cell:	n/a	chr9:105015565-105015573
21	CTCF	chr9:104973540-104973690	GM12871	blood:	n/a	n/a
22	CTCF	chr9:105015540-105015690	WERI-Rb-1	eye:	n/a	chr9:105015565-105015573
23	CTCF	chr9:104962715-104962785	K562	blood:	n/a	n/a
24	CTCF	chr9:105007369-105007413	GM20000	blood:	n/a	n/a
25	CTCF	chr9:105029673-105029679	GM10248	blood:	n/a	n/a
26	CTCF	chr9:105015460-105015610	MCF-7	breast:	n/a	chr9:105015565-105015573
27	CTCF	chr9:105018830-105018903	GM10266	blood:	n/a	n/a
28	E2F4	chr9:105006785-105007034	MCF10A-Er-Src	breast:	n/a	n/a
29	E2F4	chr9:105018969-105019169	MCF10A-Er-Src	breast:	n/a	n/a
30	E2F4	chr9:105041290-105041457	MCF10A-Er-Src	breast:	n/a	n/a
31	E2F4	chr9:104995456-104995731	MCF10A-Er-Src	breast:	n/a	n/a
32	E2F4	chr9:105025079-105025217	MCF10A-Er-Src	breast:	n/a	n/a
33	E2F4	chr9:105036415-105036556	MCF10A-Er-Src	breast:	n/a	n/a
34	E2F4	chr9:104957984-104958085	MCF10A-Er-Src	breast:	n/a	n/a
35	E2F4	chr9:104953369-104953678	MCF10A-Er-Src	breast:	n/a	n/a
36	EGR1	chr9:104985711-104985905	K562	blood:	n/a	n/a
37	EGR1	chr9:104999892-105000088	K562	blood:	n/a	n/a
38	EGR1	chr9:104999898-105000117	K562	blood:	n/a	n/a
39	ELK1	chr9:104988531-104988544	GM12878	blood:	n/a	n/a
40	EP300	chr9:104999780-104999807	GM12878	blood:	n/a	n/a
41	EP300	chr9:104944651-104944698	K562	blood:	n/a	n/a
42	EP300	chr9:104988376-104988646	K562	blood:	n/a	chr9:104988379-104988393
43	EP300	chr9:105026378-105026917	GM12878	blood:	n/a	chr9:105026435-105026449
44	ESR1	chr9:104949808-104950300	ECC-1	luminal epithelium:	n/a	n/a
45	ESR1	chr9:104949747-104950237	ECC-1	luminal epithelium:	n/a	n/a
46	ESR1	chr9:104949861-104950228	ECC-1	luminal epithelium:	n/a	n/a
47	ESR1	chr9:104949674-104950198	ECC-1	luminal epithelium:	n/a	n/a
48	FOS	chr9:105036291-105036608	MCF10A-Er-Src	breast:	n/a	chr9:105036451-105036460
49	FOS	chr9:105036246-105036626	MCF10A-Er-Src	breast:	n/a	chr9:105036451-105036460
50	FOS	chr9:105017647-105017981	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr9:104998428..105001146-chr9:105002179..105004444,3	K562	blood:
2	chr9:104998428..105001146-chr9:105002179..105004444,3	K562	blood:
3	chr9:104973156..104974681-chr9:104986450..104988784,2	MCF-7	breast:
4	chr9:104996734..105000664-chr9:105001906..105004565,3	K562	blood:
5	chr9:104996734..105000664-chr9:105001906..105004565,3	K562	blood:
6	chr10:9229922..9230664-chr9:104997433..104997933,2	MCF-7	breast:
7	chr9:104973156..104974681-chr9:104986450..104988784,2	MCF-7	breast:

(count:19 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf107-5	chr9:105045829-105045892	NONHSAT133761
2	lnc-C9orf107-6	chr9:105022537-105022537	FPKM1_group_33627_transcript_2
3	lnc-C9orf107-6	chr9:105022063-105022447	FPKM1_group_33627_transcript_2
4	lnc-GRIN3A-3	chr9:105029817-105029914	NONHSAT133756
5	lnc-C9orf107-6	chr9:105022063-105022447	NONHSAT133760
6	lnc-GRIN3A-3	chr9:104946414-104946469	ucscGeneNc_uc004bbt_2
7	lnc-C9orf107-2	chr9:104997351-104999003	FPKM1_group_33624_transcript_3
8	lnc-GRIN3A-3	chr9:104946414-104946469	NONHSAT133756
9	lnc-GRIN3A-3	chr9:104942626-104945366	NONHSAT133756
10	lnc-C9orf107-2	chr9:104998737-104998845	XLOC_007494
11	lnc-C9orf107-2	chr9:104997647-104997890	FPKM1_group_33624_transcript_3
12	lnc-C9orf107-6	chr9:105022537-105022636	NONHSAT133760
13	lnc-GRIN3A-3	chr9:104990149-104990219	NONHSAT133756
14	lnc-C9orf107-2	chr9:105000311-105000554	NONHSAT133757
15	lnc-C9orf107-2	chr9:105000314-105000407	XLOC_007494
16	lnc-C9orf107-2	chr9:104997351-104999003	NONHSAT133757
17	lnc-GRIN3A-3	chr9:105029817-105029914	ucscGeneNc_uc004bbt_2
18	lnc-GRIN3A-3	chr9:104990149-104990219	ucscGeneNc_uc004bbt_2
19	lnc-GRIN3A-3	chr9:104942631-104945366	ucscGeneNc_uc004bbt_2

No data

Variant related genes	Relation type
RNU6-329P	TF binding region

Extended variants
information (count: 1108 )
Associated
traits (count: 67 )

Variant overlapped rSNPs/rCNVs (count:1108 , 50 per page) page: 1 2 3 4 5 6 7 ... 23

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs320205	chr9:104943675-104943676	Inactive region	lncRNA	n/a	Overlapped CNVs	mRNA abundance
2	rs576309364	chr9:104943720-104943721	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs192426525	chr9:104943726-104943727	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs567403260	chr9:104943727-104943728	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
5	rs370745145	chr9:104943730-104943731	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
6	rs183292230	chr9:104943732-104943733	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
7	rs375563584	chr9:104943734-104943735	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
8	rs528293208	chr9:104943739-104943740	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
9	rs10989889	chr9:104943755-104943756	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
10	rs148375606	chr9:104943767-104943768	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
11	rs537116373	chr9:104943772-104943773	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
12	rs544274890	chr9:104943785-104943786	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
13	rs577952021	chr9:104943791-104943792	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
14	rs140630771	chr9:104943796-104943797	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
15	rs540430815	chr9:104943805-104943806	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
16	rs560842669	chr9:104943809-104943810	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
17	rs150487449	chr9:104943815-104943816	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
18	rs137869773	chr9:104943819-104943820	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
19	rs545396882	chr9:104943831-104943832	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
20	rs564179978	chr9:104943835-104943836	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
21	rs188738022	chr9:104943836-104943837	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
22	rs536148552	chr9:104943847-104943848	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
23	rs372647720	chr9:104943853-104943854	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
24	rs562447210	chr9:104943854-104943855	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
25	rs320206	chr9:104943859-104943860	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs551493887	chr9:104943863-104943864	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
27	rs549969586	chr9:104943866-104943867	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
28	rs547967739	chr9:104943872-104943873	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
29	rs547250133	chr9:104943876-104943877	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
30	rs376398044	chr9:104943883-104943884	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
31	rs567565115	chr9:104943916-104943917	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
32	rs568042845	chr9:104943920-104943921	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
33	rs529129693	chr9:104943935-104943936	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
34	rs549384562	chr9:104943947-104943948	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
35	rs7858263	chr9:104943956-104943957	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs530713222	chr9:104943959-104943960	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
37	rs192529152	chr9:104943969-104943970	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
38	rs182565769	chr9:104943973-104943974	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
39	rs320207	chr9:104943986-104943987	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs369831016	chr9:104943997-104943998	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
41	rs62580024	chr9:104944001-104944002	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
42	rs556003958	chr9:104944003-104944004	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
43	rs666456	chr9:104944004-104944005	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs554058801	chr9:104944006-104944007	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
45	rs201648395	chr9:104944017-104944018	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
46	rs574304466	chr9:104944019-104944020	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
47	rs199679273	chr9:104944024-104944025	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
48	rs78531466	chr9:104944034-104944035	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
49	rs76524321	chr9:104944035-104944036	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
50	rs74683808	chr9:104944046-104944047	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:67)

Disease	PMID	Source
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Medulloblastoma	21979893	CNVD
microdeletion syndrome	16199537	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Cancer	20164919	CNVD
Urothelial carcinoma	21177765	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Cancer	16751803	CNVD
Myelofibrosis	22110671	CNVD
lymphocytic leukemia	21291569	CNVD
Leukemia	17361228	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Glioblastoma	16823260	CNVD
Leukemia	18688285	CNVD
Non-small cell lung cancer	21044232	CNVD
Brain cancer	20823417	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Astrocytoma	17387387	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Renal cell carcinoma	19461508	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Heart disease	21282601	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Lung cancer	18438408	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute myeloid leukemia	21251322	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral cancer	21386901	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Prostate cancer	18632612	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Gastric cancer	17908304	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
small cell lung cancer	20016488	CNVD
Cardiac fibroma	18329553	CNVD
Breast cancer	17133270	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Fukuyama congenital muscular dystrophy	21572526	CNVD
Testicular germ cell tumor	18059402	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Mantle cell lymphoma	19029149	CNVD
Intracranial aneurysm	16715129	CNVD
Neuroblastoma	20406844	CNVD
Schizophrenia	23813976	CNVD
Basal cell lymphoma	21115979	CNVD

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104947400-104950200	Enhancers	Fetal Heart	heart
2	chr9:104947800-104948000	Enhancers	Ovary	ovary
3	chr9:104947800-104948400	Enhancers	Stomach Smooth Muscle	stomach
4	chr9:104947800-104948800	Enhancers	Adipose Nuclei	Adipose
5	chr9:104948000-104948800	Enhancers	Fetal Kidney	kidney
6	chr9:104948200-104948800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:104948600-104949200	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr9:104948800-104949800	Weak transcription	Fetal Kidney	kidney
9	chr9:104949200-104949600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr9:104949600-104950400	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr9:104950000-104950200	Enhancers	Fetal Kidney	kidney
12	chr9:104950000-104950800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr9:104950000-104950800	Enhancers	Ovary	ovary
14	chr9:104971400-104971800	Active TSS	Aorta	Aorta
15	chr9:104985600-104986200	Active TSS	H1 Cell Line	embryonic stem cell
16	chr9:104985600-104986200	Active TSS	H9 Cell Line	embryonic stem cell
17	chr9:104985600-104986200	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr9:104985600-104986200	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr9:104985600-104986200	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr9:104985600-104986200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr9:104985600-104986200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:104985600-104986400	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr9:104985600-104986400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:104985600-104986600	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr9:104985600-104986600	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr9:104985800-104986200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr9:104985800-104986200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr9:104985800-104986200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr9:104985800-104986400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr9:104985800-104986400	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr9:104985800-104986400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr9:104985800-104986400	Active TSS	Liver	Liver
33	chr9:104985800-104986400	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr9:104985800-104986400	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr9:104985800-104986600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr9:104986200-104986400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
37	chr9:104986200-104986400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr9:104986200-104986600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr9:104986200-104986600	Active TSS	K562	blood
40	chr9:104986200-104986800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
41	chr9:104986400-104986600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr9:104986400-104986600	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr9:104986400-104986600	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr9:104986600-104987000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr9:104986600-104988800	Weak transcription	K562	blood
46	chr9:104988000-104989000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr9:104988400-104988800	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr9:104988800-104989000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr9:104988800-104989200	Enhancers	Fetal Intestine Large	intestine
50	chr9:104988800-104989200	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links