Variant report

Variant	nsv508634
Chromosome Location	chr11:58624088-58657382
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	ARID3A	chr11:58648155-58648546	HepG2	liver:	n/a	n/a
2	BATF	chr11:58634982-58635318	GM12878	blood:	n/a	n/a
3	CEBPB	chr11:58656053-58656436	HepG2	liver:	n/a	chr11:58656264-58656275 chr11:58656231-58656242 chr11:58656213-58656224
4	CEBPB	chr11:58656150-58656434	MCF-7	breast:	n/a	chr11:58656264-58656275 chr11:58656231-58656242 chr11:58656213-58656224
5	CEBPB	chr11:58648139-58648384	HepG2	liver:	n/a	chr11:58648287-58648300
6	CEBPB	chr11:58627346-58627618	HepG2	liver:	n/a	chr11:58627487-58627498
7	CEBPB	chr11:58656076-58656380	IMR90	lung:	n/a	chr11:58656264-58656275 chr11:58656231-58656242 chr11:58656213-58656224
8	CEBPB	chr11:58648024-58648392	HepG2	liver:	n/a	chr11:58648287-58648300
9	CEBPB	chr11:58648074-58648804	HepG2	liver:	n/a	chr11:58648287-58648300
10	CEBPB	chr11:58627355-58627619	A549	lung:	n/a	chr11:58627487-58627498
11	CEBPB	chr11:58656127-58656438	K562	blood:	n/a	chr11:58656264-58656275 chr11:58656231-58656242 chr11:58656213-58656224
12	CEBPB	chr11:58656689-58656951	HepG2	liver:	n/a	n/a
13	CEBPB	chr11:58656085-58656389	Hela-S3	cervix:	n/a	chr11:58656264-58656275 chr11:58656231-58656242 chr11:58656213-58656224
14	CEBPB	chr11:58648118-58648482	HepG2	liver:	n/a	chr11:58648287-58648300
15	CEBPB	chr11:58648183-58648434	A549	lung:	n/a	chr11:58648287-58648300
16	CEBPB	chr11:58656131-58656456	MCF-7	breast:	n/a	chr11:58656264-58656275 chr11:58656231-58656242 chr11:58656213-58656224
17	CEBPB	chr11:58656078-58656414	A549	lung:	n/a	chr11:58656264-58656275 chr11:58656231-58656242 chr11:58656213-58656224
18	CTCF	chr11:58629197-58629233	GM20000	blood:	n/a	n/a
19	CTCF	chr11:58635180-58635330	NHEK	skin:	n/a	n/a
20	CTCF	chr11:58635260-58635410	HMEC	breast:	n/a	chr11:58635322-58635331
21	CTCF	chr11:58635227-58635452	NHEK	skin:	n/a	chr11:58635322-58635331
22	CTCF	chr11:58635240-58635390	NHEK	skin:	n/a	chr11:58635322-58635331
23	CTCF	chr11:58639263-58639310	Fibrobl	skin:	n/a	n/a
24	E2F4	chr11:58656116-58656334	MCF10A-Er-Src	breast:	n/a	n/a
25	EP300	chr11:58656250-58656296	HepG2	liver:	n/a	n/a
26	EP300	chr11:58648140-58648429	HepG2	liver:	n/a	n/a
27	EP300	chr11:58648078-58648464	HepG2	liver:	n/a	n/a
28	EP300	chr11:58648032-58648406	HepG2	liver:	n/a	n/a
29	FOS	chr11:58656123-58656407	MCF10A-Er-Src	breast:	n/a	n/a
30	FOS	chr11:58656221-58656332	MCF10A-Er-Src	breast:	n/a	n/a
31	FOS	chr11:58635070-58635352	MCF10A-Er-Src	breast:	n/a	n/a
32	FOS	chr11:58656108-58656379	MCF10A-Er-Src	breast:	n/a	n/a
33	FOS	chr11:58635057-58635323	MCF10A-Er-Src	breast:	n/a	n/a
34	FOS	chr11:58656101-58656372	MCF10A-Er-Src	breast:	n/a	n/a
35	FOS	chr11:58634999-58635414	MCF10A-Er-Src	breast:	n/a	n/a
36	FOS	chr11:58635123-58635280	MCF10A-Er-Src	breast:	n/a	n/a
37	FOXA1	chr11:58647950-58648372	HepG2	liver:	n/a	n/a
38	FOXA1	chr11:58648036-58648475	HepG2	liver:	n/a	n/a
39	FOXA1	chr11:58647976-58648544	HepG2	liver:	n/a	n/a
40	FOXA1	chr11:58656069-58656456	HepG2	liver:	n/a	n/a
41	FOXA1	chr11:58648027-58648516	HepG2	liver:	n/a	n/a
42	FOXA2	chr11:58647992-58648393	HepG2	liver:	n/a	n/a
43	FOXA2	chr11:58647895-58648633	HepG2	liver:	n/a	n/a
44	FOXA2	chr11:58644286-58644682	A549	lung:	n/a	n/a
45	FOXA2	chr11:58656121-58656379	HepG2	liver:	n/a	n/a
46	GATA3	chr11:58648189-58648326	SH-SY5Y	brain:	n/a	n/a
47	HDAC2	chr11:58648041-58648453	HepG2	liver:	n/a	n/a
48	HDAC2	chr11:58648138-58648463	HepG2	liver:	n/a	n/a
49	HNF4A	chr11:58648083-58648385	HepG2	liver:	n/a	chr11:58648324-58648339 chr11:58648325-58648338 chr11:58648326-58648338 chr11:58648324-58648339 chr11:58648326-58648338 chr11:58648324-58648339 chr11:58648324-58648339 chr11:58648326-58648338 chr11:58648324-58648339
50	HNF4A	chr11:58648110-58648399	HepG2	liver:	n/a	chr11:58648324-58648339 chr11:58648325-58648338 chr11:58648326-58648338 chr11:58648324-58648339 chr11:58648326-58648338 chr11:58648324-58648339 chr11:58648324-58648339 chr11:58648326-58648338 chr11:58648324-58648339

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:58651984-58652034	SK-N-SH	brain:	n/a
2	chr11:58651984-58652034	SK-N-MC	brain:	n/a
3	chr11:58651984-58652034	BJ	skin:	n/a
4	chr11:58651984-58652034	CMK	blood:	n/a
5	chr11:58651984-58652034	HIPEpiC	eye:	n/a
6	chr11:58651984-58652034	ProgFib	skin:	n/a
7	chr11:58651984-58652034	MCF-7	breast:	n/a
8	chr11:58651984-58652034	AG10803	skin:	n/a
9	chr11:58651984-58652034	GM06990	blood:	n/a
10	chr11:58651984-58652034	Caco-2	colon:	n/a
11	chr11:58651984-58652034	PANC-1	pancreas:	n/a
12	chr11:58651984-58652034	HCM	heart:	n/a
13	chr11:58651984-58652034	NHBE	bronchial:	n/a
14	chr11:58651984-58652034	A549	lung:	n/a
15	chr11:58651984-58652034	Hela-S3	cervix:	n/a
16	chr11:58651984-58652034	GM12892	blood:	n/a
17	chr11:58651984-58652034	AG09309	skin:	n/a
18	chr11:58651984-58652034	HRPEpiC	eye:	n/a
19	chr11:58651984-58652034	HAEpiC	amniotic membrane:	n/a
20	chr11:58651984-58652034	GM19239	blood:	n/a
21	chr11:58651984-58652034	LNCaP	prostate:	n/a
22	chr11:58651984-58652034	HEEpiC	esophagus:	n/a
23	chr11:58651984-58652034	HMEC	breast:	n/a
24	chr11:58651984-58652034	SK-N-SH_RA	brain:	n/a
25	chr11:58651984-58652034	PrEC	prostate:	n/a
26	chr11:58651984-58652034	SAEC	small airway:	n/a
27	chr11:58651984-58652034	T-47D	breast:	n/a
28	chr11:58651984-58652034	HEK293	kidney:	embryo
29	chr11:58651984-58652034	HCPEpiC	choroid plexus:	n/a
30	chr11:58651984-58652034	GM12878	blood:	n/a
31	chr11:58651984-58652034	HRCEpiC	kidney:	n/a
32	chr11:58651984-58652034	HepG2	liver:	n/a
33	chr11:58651984-58652034	AoSMC	blood vessel:	n/a
34	chr11:58651984-58652034	HPAEpiC	pulmonary alveolar:	n/a
35	chr11:58651984-58652034	RPTEC	kidney:	n/a
36	chr11:58651984-58652034	HRE	kidney:	n/a
37	chr11:58651984-58652034	IMR90	lung:	fetal
38	chr11:58651984-58652034	NB4	blood:	n/a
39	chr11:58651984-58652034	HL-60	blood:	n/a
40	chr11:58651984-58652034	MCF10A-Er-Src	breast:	n/a
41	chr11:58651984-58652034	HUVEC	blood vessel:	n/a
42	chr11:58651984-58652034	AG04449	skin:	fetal
43	chr11:58651984-58652034	ovcar-3	ovarian:	n/a
44	chr11:58651984-58652034	AG04450	lung:	fetal
45	chr11:58651984-58652034	AG09319	gingival:	n/a
46	chr11:58651984-58652034	ECC-1	luminal epithelium:	n/a
47	chr11:58651984-58652034	Jurkat	blood:	n/a
48	chr11:58651984-58652034	HCT-116	colon:	n/a
49	chr11:58651984-58652034	NH-A	brain:	n/a
50	chr11:58651984-58652034	HNPCEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:58346639..58348965-chr11:58654113..58656554,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLYATL1-1	chr11:58645775-58645854	ENSG00000254717
2	lnc-GLYATL1-1	chr11:58652424-58652497	NONHSAT021485
3	lnc-GLYAT-1	chr11:58656261-58656370	l_477_chr11:58656260-58660325_ovary
4	lnc-GLYAT-1	chr11:58656394-58657698	l_477_chr11:58656260-58660325_ovary
5	lnc-GLYATL1-1	chr11:58652379-58652497	ENSG00000254717

Variant related genes	Relation type
GLYATL1P2	TF binding region
GLYATL1P2	CpG island
ENSG00000255073	chromatin interactions

Extended variants
information (count: 1163 )
Associated
traits (count: 54 )

Variant overlapped rSNPs/rCNVs (count:1163 , 50 per page) page: 1 2 3 4 5 6 7 ... 24

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs112051470	chr11:58624096-58624097	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs531920512	chr11:58624140-58624141	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs185961735	chr11:58624152-58624153	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs564966475	chr11:58624160-58624161	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs546281588	chr11:58624163-58624164	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs599275	chr11:58624169-58624170	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs599254	chr11:58624180-58624181	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs566168761	chr11:58624210-58624211	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs190675221	chr11:58624255-58624256	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs369701367	chr11:58624259-58624260	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs369177017	chr11:58624261-58624262	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs548408160	chr11:58624270-58624271	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs548588953	chr11:58624281-58624282	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs569952051	chr11:58624327-58624328	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs598767	chr11:58624339-58624340	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs377571910	chr11:58624357-58624358	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs143236465	chr11:58624367-58624368	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs534618343	chr11:58624387-58624388	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs370484671	chr11:58624391-58624392	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs374935404	chr11:58624397-58624398	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs552745490	chr11:58624431-58624432	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs386753948	chr11:58624447-58624448	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs574520311	chr11:58624455-58624456	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs367597360	chr11:58624459-58624460	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs536244389	chr11:58624471-58624472	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs571852584	chr11:58624484-58624485	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs374750572	chr11:58624492-58624493	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs678880	chr11:58624496-58624497	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs543674755	chr11:58624514-58624515	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs565247490	chr11:58624605-58624606	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs148309750	chr11:58624625-58624626	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs678346	chr11:58624631-58624632	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs4103678	chr11:58624711-58624712	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs34018567	chr11:58624753-58624754	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs34068885	chr11:58624756-58624757	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs398097559	chr11:58624762-58624763	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs2856258	chr11:58624783-58624784	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs576050	chr11:58624800-58624801	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs564228687	chr11:58631000-58631001	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
40	rs587953	chr11:58631001-58631002	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs492802	chr11:58631023-58631024	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs113040048	chr11:58631078-58631079	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs493659	chr11:58631089-58631090	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs550276403	chr11:58631149-58631150	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs569873535	chr11:58631181-58631182	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs116573974	chr11:58631185-58631186	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
47	rs144334796	chr11:58631190-58631191	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
48	rs559199100	chr11:58631252-58631253	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs561197502	chr11:58631272-58631273	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs573063727	chr11:58631289-58631290	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:54)

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
Non-syndromic sensorineural hearing loss	17122850	CNVD
Cancer	20164919	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58623800-58624800	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr11:58631000-58631400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:58631000-58631400	ZNF genes & repeats	Thymus	Thymus
4	chr11:58631200-58631400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr11:58631400-58635000	Enhancers	Thymus	Thymus
6	chr11:58631600-58632400	Enhancers	Fetal Thymus	thymus
7	chr11:58632400-58632800	Weak transcription	Fetal Thymus	thymus
8	chr11:58632800-58634600	Enhancers	Fetal Thymus	thymus
9	chr11:58633800-58634000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr11:58634000-58634800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:58634000-58635800	Enhancers	NHEK	skin
12	chr11:58634200-58634600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr11:58634200-58635600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:58634400-58635000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr11:58634400-58635600	Enhancers	HMEC	breast
16	chr11:58634800-58635400	Enhancers	NHDF-Ad	bronchial
17	chr11:58634800-58635600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:58635000-58635600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr11:58635000-58636000	Weak transcription	Thymus	Thymus
20	chr11:58635000-58668000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr11:58635600-58637600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr11:58636000-58636200	Enhancers	Thymus	Thymus
23	chr11:58637600-58638200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr11:58638200-58638400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr11:58643600-58644800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
26	chr11:58645400-58645600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
27	chr11:58645400-58646400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
28	chr11:58645600-58652400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr11:58647600-58649000	Enhancers	Liver	Liver
30	chr11:58647600-58649000	Enhancers	HepG2	liver
31	chr11:58647800-58648000	Enhancers	Fetal Intestine Small	intestine
32	chr11:58648000-58654400	Weak transcription	Fetal Lung	lung
33	chr11:58648000-58655000	Weak transcription	Fetal Intestine Small	intestine
34	chr11:58651000-58671200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr11:58651400-58660200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:58652400-58653200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr11:58652600-58653400	ZNF genes & repeats	Fetal Stomach	stomach
38	chr11:58653200-58661400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr11:58654400-58654800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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