Variant report

Variant	nsv515922
Chromosome Location	chrX:5602110-5666329
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	BCL3	chrX:5644229-5644536	GM12878	blood:	n/a	n/a
2	BHLHE40	chrX:5621079-5621094	GM12878	blood:	n/a	n/a
3	CEBPB	chrX:5640908-5641229	HepG2	liver:	n/a	chrX:5641078-5641091
4	CEBPB	chrX:5620596-5620796	A549	lung:	n/a	n/a
5	CEBPB	chrX:5640967-5641230	IMR90	lung:	n/a	chrX:5641078-5641091
6	CEBPB	chrX:5620589-5620819	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chrX:5603357-5603361	GM10248	blood:	n/a	n/a
8	CTCF	chrX:5649386-5649467	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chrX:5662323-5662339	GM10248	blood:	n/a	n/a
10	CTCF	chrX:5614063-5614150	GM20000	blood:	n/a	n/a
11	CTCF	chrX:5610476-5610512	GM10248	blood:	n/a	n/a
12	CTCF	chrX:5649654-5649768	Medullo	brain:	n/a	n/a
13	CTCF	chrX:5662342-5662403	GM10248	blood:	n/a	n/a
14	CTCF	chrX:5618636-5618711	GM20000	blood:	n/a	n/a
15	CTCF	chrX:5636246-5636266	GM19239	blood:	n/a	n/a
16	CTCF	chrX:5603109-5603143	GM12891	blood:	n/a	n/a
17	CTCF	chrX:5617138-5617169	GM10266	blood:	n/a	n/a
18	CTCF	chrX:5621356-5621427	GM10266	blood:	n/a	n/a
19	CTCF	chrX:5613407-5613428	GM10266	blood:	n/a	n/a
20	CTCF	chrX:5660751-5660843	LNCaP	prostate:	n/a	n/a
21	CTCF	chrX:5618461-5618477	Medullo	brain:	n/a	n/a
22	CTCF	chrX:5607139-5607202	GM10248	blood:	n/a	n/a
23	CTCF	chrX:5656166-5656250	GM20000	blood:	n/a	n/a
24	CTCF	chrX:5648227-5648326	GM10248	blood:	n/a	n/a
25	CTCF	chrX:5618485-5618496	Medullo	brain:	n/a	n/a
26	CTCF	chrX:5654412-5654473	GM20000	blood:	n/a	n/a
27	CTCF	chrX:5649335-5649407	GM10248	blood:	n/a	n/a
28	E2F4	chrX:5648171-5648414	MCF10A-Er-Src	breast:	n/a	n/a
29	E2F4	chrX:5625243-5625420	MCF10A-Er-Src	breast:	n/a	n/a
30	E2F6	chrX:5649226-5649653	H1-hESC	embryonic stem cell:	n/a	n/a
31	FAM48A	chrX:5642069-5642265	GM12878	blood:	n/a	n/a
32	FAM48A	chrX:5607326-5607497	GM12878	blood:	n/a	n/a
33	FOXM1	chrX:5644211-5644580	GM12878	blood:	n/a	n/a
34	GATA2	chrX:5656985-5657309	K562	blood:	n/a	n/a
35	IRF3	chrX:5620185-5620195	GM12878	blood:	n/a	n/a
36	MAFF	chrX:5642183-5642494	HepG2	liver:	n/a	chrX:5642354-5642372
37	MAFF	chrX:5642258-5642416	K562	blood:	n/a	chrX:5642354-5642372
38	MAFK	chrX:5642197-5642454	Hela-S3	cervix:	n/a	chrX:5642360-5642371 chrX:5642360-5642371 chrX:5642359-5642370 chrX:5642359-5642370 chrX:5642355-5642370
39	MAFK	chrX:5657004-5657070	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAFK	chrX:5642230-5642503	K562	blood:	n/a	chrX:5642360-5642371 chrX:5642360-5642371 chrX:5642359-5642370 chrX:5642359-5642370 chrX:5642355-5642370
41	MAFK	chrX:5642178-5642546	IMR90	lung:	n/a	chrX:5642360-5642371 chrX:5642360-5642371 chrX:5642359-5642370 chrX:5642359-5642370 chrX:5642355-5642370
42	MAFK	chrX:5665462-5665704	HepG2	liver:	n/a	chrX:5665625-5665636
43	MAFK	chrX:5642250-5642450	H1-hESC	embryonic stem cell:	n/a	chrX:5642360-5642371 chrX:5642360-5642371 chrX:5642359-5642370 chrX:5642359-5642370 chrX:5642355-5642370
44	MAFK	chrX:5642184-5642544	HepG2	liver:	n/a	chrX:5642360-5642371 chrX:5642360-5642371 chrX:5642359-5642370 chrX:5642359-5642370 chrX:5642355-5642370
45	MAFK	chrX:5642217-5642523	HepG2	liver:	n/a	chrX:5642360-5642371 chrX:5642360-5642371 chrX:5642359-5642370 chrX:5642359-5642370 chrX:5642355-5642370
46	MYC	chrX:5614734-5615088	MCF10A-Er-Src	breast:	n/a	n/a
47	MYC	chrX:5660701-5660730	H1-hESC	embryonic stem cell:	n/a	n/a
48	MYC	chrX:5648026-5648089	H1-hESC	embryonic stem cell:	n/a	n/a
49	MYC	chrX:5665887-5666139	MCF10A-Er-Src	breast:	n/a	n/a
50	MYC	chrX:5657039-5657102	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:5642806..5644817-chrX:5646712..5648581,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NLGN4X-2	chrX:5653971-5653998	NONHSAT136159
2	lnc-NLGN4X-2	chrX:5653971-5654414	l_3885_chrX:5647214-5654414_placenta
3	lnc-NLGN4X-2	chrX:5653971-5654346	NONHSAT136158
4	lnc-NLGN4X-1	chrX:5643971-5643998	ENSG00000236120
5	lnc-NLGN4X-2	chrX:5647215-5647913	l_3885_chrX:5647214-5654414_placenta
6	lnc-NLGN4X-2	chrX:5654071-5654121	NONHSAT136160
7	lnc-NLGN4X-1	chrX:5644071-5644121	ENSG00000236120

Variant related genes	Relation type
ENSG00000236120	TF binding region
ENSG00000236120	chromatin interactions

Extended variants
information (count: 366 )
Associated
traits (count: 49 )

Variant overlapped rSNPs/rCNVs (count:366 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs182680373	chrX:5611428-5611429	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs185871431	chrX:5611558-5611559	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs553074796	chrX:5611619-5611620	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs11094800	chrX:5611715-5611716	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs112285912	chrX:5611821-5611822	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs189803324	chrX:5611910-5611911	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs182413635	chrX:5611929-5611930	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs375300657	chrX:5611957-5611958	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs139964982	chrX:5611984-5611985	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs188671740	chrX:5612114-5612115	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs192365581	chrX:5612146-5612147	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs6639465	chrX:5612207-5612208	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs114684431	chrX:5612214-5612215	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs578067385	chrX:5612380-5612381	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs6638536	chrX:5612415-5612416	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs116103997	chrX:5612463-5612464	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs145112537	chrX:5612578-5612579	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs183689919	chrX:5613639-5613640	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs151140891	chrX:5613753-5613754	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs111315905	chrX:5613816-5613817	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
21	rs141947256	chrX:5613839-5613840	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
22	rs12688400	chrX:5613882-5613883	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
23	rs12690199	chrX:5613995-5613996	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
24	rs183951520	chrX:5625403-5625404	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs151331477	chrX:5625482-5625483	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs187139584	chrX:5625514-5625515	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs369834943	chrX:5625643-5625644	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs5916223	chrX:5625774-5625775	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs544187243	chrX:5625798-5625799	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs4826804	chrX:5625806-5625807	Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs16983822	chrX:5625887-5625888	Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs532818759	chrX:5625920-5625921	Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs191183101	chrX:5625924-5625925	Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs377730356	chrX:5625985-5625986	Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs371678224	chrX:5626032-5626033	Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs183686537	chrX:5626155-5626156	Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs146555945	chrX:5626175-5626176	Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs5022865	chrX:5626252-5626253	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs546213403	chrX:5626315-5626316	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs537248650	chrX:5626451-5626452	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs141297231	chrX:5626468-5626469	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs111993137	chrX:5626472-5626473	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs372425766	chrX:5626545-5626546	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs548374666	chrX:5626604-5626605	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs190490721	chrX:5626672-5626673	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs568173366	chrX:5626743-5626744	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs182146091	chrX:5626766-5626767	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs377555606	chrX:5626810-5626811	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs185882088	chrX:5626826-5626827	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs113066975	chrX:5626840-5626841	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:49)

Disease	PMID	Source
short stature	22470819	CNVD
turner syndrome	20877625	CNVD
Kallmann Syndrome 1	22470819	CNVD
Oro-facial digital syndrome	19023858	CNVD
Oro-facial digital syndrome	21572526	CNVD
Aicardi syndrome	21572526	CNVD
Vermis hypoplasia	21569638	CNVD
Opitz syndrome	21569638	CNVD
Opitz syndrome	21572526	CNVD
Oro-facial digital syndrome	21569638	CNVD
Abnormal corpus callosum	21572526	CNVD
T-cell lymphomas	19863542	CNVD
Glioblastoma multiforme	21080181	CNVD
Breast cancer	17603634	CNVD
Seminomas	18059402	CNVD
abnormal development	18461090	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Cancer	21637783	CNVD
Glioblastoma multiforme	19960244	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Cancer	16751803	CNVD
Intellectual disability	23615299	CNVD
Neuroblastoma	18923191	CNVD
Burkitt''s lymphoma	20823134	CNVD
Astrocytoma	17387387	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Metanephric adenoma	20802469	CNVD
Medulloblastoma	21979893	CNVD
Schizophrenia	23904455	CNVD
Olfactory neuroblastoma	18408657	CNVD
infertile	22614455	CNVD
small cell lung cancer	20016488	CNVD
Acute myeloid leukemia	20729466	CNVD
Mental retardation	17406619	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Glioblastoma multiforme	22286061	CNVD
Acute myeloid leukemia	21251322	CNVD
Cancer	20581869	CNVD
Lung cancer	18438408	CNVD
Multiple myeloma	20724749	CNVD
Breast cancer	21858162	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Breast cancer	21785460	CNVD
XY gonadal dysgenesis	20685758	CNVD
Breast cancer	21364760	CNVD
Mental retardation	20486941	CNVD

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:5611400-5611800	Enhancers	H9 Cell Line	embryonic stem cell
2	chrX:5611400-5612000	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chrX:5611400-5612600	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chrX:5611600-5612200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chrX:5613600-5613800	Enhancers	Fetal Brain Male	brain
6	chrX:5613800-5614000	Bivalent Enhancer	Fetal Brain Male	brain
7	chrX:5625400-5625800	Enhancers	Brain Inferior Temporal Lobe	brain
8	chrX:5625400-5625800	Enhancers	Brain Substantia Nigra	brain
9	chrX:5625400-5626000	Enhancers	Brain Hippocampus Middle	brain
10	chrX:5625400-5626400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chrX:5625800-5626200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chrX:5625800-5626200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
13	chrX:5625800-5626200	Active TSS	Brain Substantia Nigra	brain
14	chrX:5625800-5626800	Enhancers	HSMM	muscle
15	chrX:5625800-5627200	Enhancers	HMEC	breast
16	chrX:5626000-5626200	Enhancers	Brain Anterior Caudate	brain
17	chrX:5626000-5626400	Enhancers	Muscle Satellite Cultured Cells	--
18	chrX:5626000-5626400	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chrX:5626000-5626400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chrX:5626000-5626800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chrX:5626000-5626800	Enhancers	NHDF-Ad	bronchial
22	chrX:5626000-5627000	Enhancers	HSMMtube	muscle
23	chrX:5626000-5627200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chrX:5626400-5631200	Weak transcription	Brain Hippocampus Middle	brain
25	chrX:5631200-5631600	Enhancers	Brain Hippocampus Middle	brain
26	chrX:5631600-5634000	Weak transcription	Fetal Heart	heart
27	chrX:5641200-5641400	Enhancers	HMEC	breast
28	chrX:5641400-5644400	Active TSS	Adipose Nuclei	Adipose
29	chrX:5642200-5644000	Active TSS	HMEC	breast
30	chrX:5643000-5643200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chrX:5643000-5643400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chrX:5643400-5645000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chrX:5643600-5644200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chrX:5643800-5644000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chrX:5643800-5644000	Enhancers	Muscle Satellite Cultured Cells	--
36	chrX:5643800-5644200	Active TSS	Rectal Mucosa Donor 29	rectum
37	chrX:5643800-5644200	Enhancers	NHDF-Ad	bronchial
38	chrX:5643800-5645200	Enhancers	Primary monocytes fromperipheralblood	blood
39	chrX:5644000-5644200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chrX:5644000-5644200	Flanking Active TSS	HMEC	breast
41	chrX:5644000-5644200	Enhancers	HSMM	muscle
42	chrX:5644000-5644400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chrX:5644000-5644400	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chrX:5644000-5644400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chrX:5644000-5644400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chrX:5644000-5644400	Enhancers	NH-A	brain
47	chrX:5644000-5645000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chrX:5644000-5645000	Enhancers	Brain Substantia Nigra	brain
49	chrX:5644200-5644400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chrX:5644200-5644400	Active TSS	HMEC	breast

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