Variant report

Variant	nsv975189
Chromosome Location	chr11:58804182-58819112
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BATF	chr11:58818940-58819193	GM12878	blood:	n/a	n/a
2	BCL11A	chr11:58818899-58819262	GM12878	blood:	n/a	chr11:58819091-58819100
3	BCL11A	chr11:58818878-58819275	GM12878	blood:	n/a	chr11:58819091-58819100
4	CTCF	chr11:58818522-58818542	GM10248	blood:	n/a	n/a
5	CTCF	chr11:58810270-58810328	GM10266	blood:	n/a	n/a
6	CTCF	chr11:58811099-58811130	GM20000	blood:	n/a	n/a
7	CTCF	chr11:58804282-58804434	Fibrobl	skin:	n/a	chr11:58804324-58804333
8	CTCF	chr11:58808800-58808858	GM13976	blood:	n/a	n/a
9	EBF1	chr11:58819020-58819064	GM12878	blood:	n/a	n/a
10	EBF1	chr11:58818874-58819172	GM12878	blood:	n/a	chr11:58819009-58819020
11	EBF1	chr11:58818897-58819240	GM12878	blood:	n/a	chr11:58819009-58819020
12	IRF4	chr11:58818851-58819323	GM12878	blood:	n/a	n/a
13	IRF4	chr11:58818900-58819294	GM12878	blood:	n/a	n/a
14	MYC	chr11:58817166-58817214	K562	blood:	n/a	n/a
15	PAX5	chr11:58818921-58819232	GM12878	blood:	n/a	chr11:58819091-58819100
16	PAX5	chr11:58818982-58819250	GM12878	blood:	n/a	chr11:58819091-58819100
17	PAX5	chr11:58818969-58819137	GM12878	blood:	n/a	chr11:58819091-58819100
18	PAX5	chr11:58818877-58819353	GM12878	blood:	n/a	chr11:58819091-58819100
19	POLR2A	chr11:58811878-58811996	ProgFib	skin:	n/a	n/a
20	POLR2A	chr11:58810380-58810458	Gliobla	brain:	n/a	n/a
21	POU2F2	chr11:58818887-58819312	GM12878	blood:	n/a	n/a
22	POU5F1	chr11:58818862-58819156	H1-hESC	embryonic stem cell:	n/a	chr11:58818991-58819005 chr11:58818992-58819006 chr11:58818991-58819005 chr11:58818991-58819005
23	SPI1	chr11:58812133-58812333	GM12891	blood:	n/a	chr11:58812249-58812262
24	SPI1	chr11:58818929-58819230	GM12878	blood:	n/a	chr11:58819091-58819100 chr11:58819093-58819106 chr11:58819095-58819104
25	SPI1	chr11:58818860-58819313	GM12891	blood:	n/a	chr11:58819091-58819100 chr11:58819093-58819106 chr11:58819095-58819104
26	SPI1	chr11:58804791-58805123	HL-60	blood:	n/a	n/a
27	SPI1	chr11:58818904-58819319	GM12878	blood:	n/a	chr11:58819091-58819100 chr11:58819093-58819106 chr11:58819095-58819104
28	SPI1	chr11:58818903-58819314	GM12891	blood:	n/a	chr11:58819091-58819100 chr11:58819093-58819106 chr11:58819095-58819104
29	SPI1	chr11:58812128-58812330	GM12891	blood:	n/a	chr11:58812249-58812262
30	SPI1	chr11:58818684-58819551	GM12878	blood:	n/a	chr11:58819091-58819100 chr11:58819093-58819106 chr11:58819095-58819104
31	SPI1	chr11:58812103-58812375	GM12878	blood:	n/a	chr11:58812249-58812262
32	STAT3	chr11:58804140-58804221	MCF10A-Er-Src	breast:	n/a	chr11:58804164-58804184

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:58810187-58810237	HRCEpiC	kidney:	n/a
2	chr11:58810187-58810237	GM12892	blood:	n/a
3	chr11:58810187-58810237	SK-N-SH	brain:	n/a
4	chr11:58806952-58807002	BE2_C	brain:	n/a
5	chr11:58806952-58807002	AG10803	skin:	n/a
6	chr11:58810187-58810237	HepG2	liver:	n/a
7	chr11:58810187-58810237	K562	blood:	n/a
8	chr11:58810187-58810237	NH-A	brain:	n/a
9	chr11:58810187-58810237	LNCaP	prostate:	n/a
10	chr11:58810187-58810237	BJ	skin:	n/a
11	chr11:58806952-58807002	HCT-116	colon:	n/a
12	chr11:58810187-58810237	GM06990	blood:	n/a
13	chr11:58810187-58810237	HAEpiC	amniotic membrane:	n/a
14	chr11:58810187-58810237	HRPEpiC	eye:	n/a
15	chr11:58810187-58810237	MCF-7	breast:	n/a
16	chr11:58806952-58807002	HL-60	blood:	n/a
17	chr11:58810187-58810237	RPTEC	kidney:	n/a
18	chr11:58810187-58810237	CMK	blood:	n/a
19	chr11:58806952-58807002	GM12892	blood:	n/a
20	chr11:58810187-58810237	AG04449	skin:	fetal
21	chr11:58806952-58807002	SAEC	small airway:	n/a
22	chr11:58810187-58810237	ProgFib	skin:	n/a
23	chr11:58810187-58810237	T-47D	breast:	n/a
24	chr11:58810187-58810237	PrEC	prostate:	n/a
25	chr11:58810187-58810237	SAEC	small airway:	n/a
26	chr11:58806952-58807002	AG04449	skin:	fetal
27	chr11:58810187-58810237	HCF	heart:	n/a
28	chr11:58806952-58807002	ProgFib	skin:	n/a
29	chr11:58806952-58807002	HCM	heart:	n/a
30	chr11:58810187-58810237	AoSMC	blood vessel:	n/a
31	chr11:58806952-58807002	HPAEpiC	pulmonary alveolar:	n/a
32	chr11:58810187-58810237	HCM	heart:	n/a
33	chr11:58806952-58807002	H1-hESC	embryonic stem cell:	embryo
34	chr11:58806952-58807002	NT2-D1	testis:	n/a
35	chr11:58806952-58807002	HNPCEpiC	eye:	n/a
36	chr11:58806952-58807002	HRCEpiC	kidney:	n/a
37	chr11:58806952-58807002	GM06990	blood:	n/a
38	chr11:58806952-58807002	ovcar-3	ovarian:	n/a
39	chr11:58810187-58810237	GM12878	blood:	n/a
40	chr11:58806952-58807002	Hela-S3	cervix:	n/a
41	chr11:58806952-58807002	HRPEpiC	eye:	n/a
42	chr11:58810187-58810237	HMEC	breast:	n/a
43	chr11:58806952-58807002	HAEpiC	amniotic membrane:	n/a
44	chr11:58806952-58807002	SK-N-MC	brain:	n/a
45	chr11:58806952-58807002	T-47D	breast:	n/a
46	chr11:58806952-58807002	SK-N-SH_RA	brain:	n/a
47	chr11:58806952-58807002	NB4	blood:	n/a
48	chr11:58810187-58810237	HEEpiC	esophagus:	n/a
49	chr11:58806952-58807002	LNCaP	prostate:	n/a
50	chr11:58810187-58810237	SK-N-MC	brain:	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLYATL2-2	chr11:58818733-58818781	ENSG00000255240.1
2	lnc-GLYATL2-2	chr11:58818733-58818781	NR_033853
3	lnc-GLYATL2-2	chr11:58818733-58818781	ENSG00000255240.1

Variant related genes	Relation type
GLYATL1P4	TF binding region
GLYATL1P4	CpG island

Extended variants
information (count: 682 )
Associated
traits (count: 53 )

Variant overlapped rSNPs/rCNVs (count:682 , 50 per page) page: 1 2 3 4 5 6 7 ... 14

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs534829447	chr11:58804245-58804246	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs530426836	chr11:58804320-58804321	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs552196708	chr11:58804402-58804403	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs116383938	chr11:58804403-58804404	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs193086314	chr11:58804410-58804411	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs138749863	chr11:58804411-58804412	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs1815851	chr11:58804427-58804428	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs1815850	chr11:58804430-58804431	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs546695251	chr11:58804473-58804474	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs28407281	chr11:58804476-58804477	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs577311502	chr11:58804535-58804536	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs536818998	chr11:58804536-58804537	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs185882040	chr11:58804554-58804555	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs545868924	chr11:58804575-58804576	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs576723558	chr11:58804629-58804630	Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs537337540	chr11:58804653-58804654	Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs189075305	chr11:58804688-58804689	Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs4938908	chr11:58804692-58804693	Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs541150921	chr11:58804726-58804727	Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs180964160	chr11:58804782-58804783	Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs574301767	chr11:58804793-58804794	Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs541961810	chr11:58804803-58804804	Flanking Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs150764798	chr11:58804837-58804838	Flanking Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs563334662	chr11:58804847-58804848	Flanking Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs2004664	chr11:58804858-58804859	Flanking Active TSS Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs1815849	chr11:58804913-58804914	Flanking Active TSS Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs564097086	chr11:58804920-58804921	Flanking Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs528061971	chr11:58804946-58804947	Flanking Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs111888353	chr11:58804953-58804954	Flanking Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs34151016	chr11:58804978-58804979	Flanking Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs139156668	chr11:58805041-58805042	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs149999699	chr11:58805051-58805052	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs562407646	chr11:58805065-58805066	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs536446856	chr11:58805067-58805068	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs548807771	chr11:58805094-58805095	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs144288089	chr11:58805147-58805148	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs537778472	chr11:58805183-58805184	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs558799280	chr11:58805185-58805186	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs71454359	chr11:58805236-58805237	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs185320693	chr11:58805272-58805273	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs34575029	chr11:58805285-58805286	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs188621842	chr11:58805289-58805290	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs574923868	chr11:58805324-58805325	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs181372041	chr11:58805325-58805326	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs563532564	chr11:58805338-58805339	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs575322623	chr11:58805339-58805340	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs186793490	chr11:58805340-58805341	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs140865657	chr11:58805341-58805342	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs528099671	chr11:58805344-58805345	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs114697322	chr11:58805393-58805394	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:53)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Gastric cancer	17908304	CNVD
Multiple myeloma	20724749	CNVD
Wilms tumour	21544195	CNVD
Autism	22495311	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Non-small cell lung cancer	21385341	CNVD
Intellectual disability	22102821	CNVD
Glioblastoma multiforme	21138945	CNVD
Esophageal cancer	21851588	CNVD
Acute myeloid leukemia	20729466	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Glioblastoma multiforme	22286061	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	21637783	CNVD
Acute myeloid leukemia	16864856	CNVD
Chronic lymphocytic leukemia	21795749	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21484798	CNVD
Ewing''s sarcoma	21437220	CNVD
Oral cancer	21386901	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	20837533	CNVD
Breast cancer	21264507	CNVD
Cervical cancer	21063398	CNVD
Glioblastoma multiforme	19960244	CNVD
Liposarcoma	21253554	CNVD
Neuroblastoma	18923524	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Neuroblastoma	17533364	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Colorectal cancer	16272173	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Pituitary adenoma	18645599	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Prostate cancer	18632612	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	21080181	CNVD
Smith-Lemli-Opitz syndrome	21572526	CNVD
Multiple myeloma	16461302	CNVD
Cancer	16751803	CNVD
Seminomas	18059402	CNVD
Autism	22495309	CNVD
Autism	20808228	CNVD
Cancer	20164919	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58782800-58810600	Weak transcription	Primary B cells from cord blood	blood
2	chr11:58803200-58804600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr11:58804400-58804600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr11:58804400-58804600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr11:58804600-58805000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr11:58804600-58806200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr11:58804600-58807400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr11:58804800-58805000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr11:58804800-58805200	Enhancers	Primary hematopoietic stem cells	blood
10	chr11:58804800-58805200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:58805000-58805200	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr11:58805000-58806200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:58805000-58825200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr11:58805200-58825400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr11:58806200-58807400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr11:58806200-58807800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr11:58807400-58808000	Strong transcription	Primary B cells from peripheral blood	blood
18	chr11:58808000-58808200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:58808000-58808600	Enhancers	Stomach Mucosa	stomach
20	chr11:58808000-58810800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr11:58810600-58811400	Strong transcription	Primary B cells from cord blood	blood
22	chr11:58810800-58811800	Strong transcription	Primary B cells from peripheral blood	blood
23	chr11:58811400-58818200	Weak transcription	Primary B cells from cord blood	blood
24	chr11:58811800-58816200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr11:58813600-58825200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:58815400-58824400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr11:58816200-58818200	Strong transcription	Primary B cells from peripheral blood	blood
28	chr11:58816600-58816800	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr11:58816800-58817000	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr11:58817000-58817200	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr11:58817000-58817200	Enhancers	Fetal Intestine Large	intestine
32	chr11:58817000-58818200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr11:58817200-58821800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr11:58817200-58825200	Weak transcription	Liver	Liver
35	chr11:58817200-58825400	Weak transcription	Fetal Intestine Large	intestine
36	chr11:58817400-58819400	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr11:58817400-58822000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr11:58818200-58818600	Genic enhancers	Primary B cells from peripheral blood	blood
39	chr11:58818200-58819400	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr11:58818200-58820200	Enhancers	Primary B cells from cord blood	blood
41	chr11:58818600-58825200	Enhancers	Primary B cells from peripheral blood	blood
42	chr11:58818800-58819400	Enhancers	GM12878-XiMat	blood

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