Variant report

Variant	nsv531042
Chromosome Location	chrX:6457403-6657810
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	ATF2	chrX:6650200-6650576	GM12878	blood:	n/a	n/a
2	ATF2	chrX:6656521-6657470	GM12878	blood:	n/a	n/a
3	ATF2	chrX:6656510-6657531	GM12878	blood:	n/a	n/a
4	BATF	chrX:6656817-6657350	GM12878	blood:	n/a	n/a
5	BATF	chrX:6656848-6657191	GM12878	blood:	n/a	n/a
6	BCL11A	chrX:6656657-6657479	GM12878	blood:	n/a	n/a
7	BCL11A	chrX:6656822-6657366	GM12878	blood:	n/a	n/a
8	BCL3	chrX:6656849-6657373	GM12878	blood:	n/a	n/a
9	BCL3	chrX:6656968-6657313	GM12878	blood:	n/a	n/a
10	BCLAF1	chrX:6656899-6657442	GM12878	blood:	n/a	n/a
11	BCLAF1	chrX:6656774-6657546	GM12878	blood:	n/a	n/a
12	BCLAF1	chrX:6650178-6650508	GM12878	blood:	n/a	n/a
13	BHLHE40	chrX:6650232-6650482	GM12878	blood:	n/a	n/a
14	BHLHE40	chrX:6656602-6657589	GM12878	blood:	n/a	n/a
15	BRCA1	chrX:6656940-6657436	GM12878	blood:	n/a	n/a
16	CEBPB	chrX:6471282-6471527	K562	blood:	n/a	chrX:6471422-6471433
17	CEBPB	chrX:6648360-6648619	HepG2	liver:	n/a	chrX:6648460-6648469 chrX:6648460-6648471
18	CEBPB	chrX:6555739-6556013	IMR90	lung:	n/a	chrX:6555877-6555888
19	CEBPB	chrX:6636411-6636698	HepG2	liver:	n/a	chrX:6636549-6636560
20	CEBPB	chrX:6524895-6525228	A549	lung:	n/a	chrX:6525062-6525075
21	CEBPB	chrX:6646348-6646551	HepG2	liver:	n/a	chrX:6646447-6646456 chrX:6646447-6646458 chrX:6646447-6646456 chrX:6646447-6646456 chrX:6646445-6646456 chrX:6646447-6646456
22	CEBPB	chrX:6656583-6657408	GM12878	blood:	n/a	n/a
23	CEBPB	chrX:6584701-6584981	IMR90	lung:	n/a	n/a
24	CEBPB	chrX:6636479-6636630	K562	blood:	n/a	chrX:6636549-6636560
25	CEBPB	chrX:6636401-6636732	IMR90	lung:	n/a	chrX:6636549-6636560
26	CEBPB	chrX:6524963-6525194	IMR90	lung:	n/a	chrX:6525062-6525075
27	CEBPB	chrX:6471293-6471471	A549	lung:	n/a	chrX:6471422-6471433
28	CEBPB	chrX:6484827-6485100	IMR90	lung:	n/a	n/a
29	CEBPB	chrX:6471257-6471479	IMR90	lung:	n/a	chrX:6471422-6471433
30	CEBPB	chrX:6555794-6556010	HepG2	liver:	n/a	chrX:6555877-6555888
31	CEBPB	chrX:6471389-6471556	HepG2	liver:	n/a	chrX:6471422-6471433
32	CEBPB	chrX:6475811-6475996	HepG2	liver:	n/a	chrX:6475939-6475950
33	CEBPB	chrX:6475740-6476115	HepG2	liver:	n/a	chrX:6475939-6475950
34	CEBPB	chrX:6636405-6636717	A549	lung:	n/a	chrX:6636549-6636560
35	CEBPB	chrX:6646306-6646609	IMR90	lung:	n/a	chrX:6646447-6646456 chrX:6646447-6646458 chrX:6646447-6646456 chrX:6646447-6646456 chrX:6646445-6646456 chrX:6646447-6646456
36	CEBPB	chrX:6648377-6648623	IMR90	lung:	n/a	chrX:6648460-6648469 chrX:6648460-6648471
37	CEBPB	chrX:6584778-6584931	A549	lung:	n/a	n/a
38	CEBPD	chrX:6622445-6623267	K562	blood:	n/a	n/a
39	CHD1	chrX:6656382-6656383	GM12878	blood:	n/a	n/a
40	CHD1	chrX:6656661-6657832	GM12878	blood:	n/a	n/a
41	CHD2	chrX:6650219-6650419	GM12878	blood:	n/a	n/a
42	CHD2	chrX:6656289-6657671	GM12878	blood:	n/a	n/a
43	CHD2	chrX:6611235-6611270	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chrX:6492935-6493084	LNCaP	prostate:	n/a	chrX:6492998-6493007 chrX:6492994-6493007 chrX:6492993-6493009 chrX:6492987-6493008 chrX:6492992-6493010
45	CTCF	chrX:6473388-6473420	GM10266	blood:	n/a	n/a
46	CTCF	chrX:6505560-6505627	Medullo	brain:	n/a	n/a
47	CTCF	chrX:6562460-6562610	MCF-7	breast:	n/a	n/a
48	CTCF	chrX:6492850-6493170	GM12878	blood:	n/a	chrX:6492998-6493007 chrX:6492994-6493007 chrX:6492993-6493009 chrX:6492987-6493008 chrX:6492992-6493010
49	CTCF	chrX:6562560-6562710	GM12871	blood:	n/a	n/a
50	CTCF	chrX:6640343-6640381	GM10248	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:6611316..6614128-chrX:6615657..6618460,2	MCF-7	breast:
2	chrX:6611316..6614128-chrX:6615657..6618460,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VCX3A-2	chrX:6595906-6596170	NONHSAT136173
2	lnc-VCX3A-2	chrX:6634384-6634507	NONHSAT136173
3	lnc-VCX3A-2	chrX:6649458-6649585	NONHSAT136173

Variant related genes	Relation type
ENSG00000231217	TF binding region
VCX3A	TF binding region

Extended variants
information (count: 1670 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:1670 , 50 per page) page: 1 2 3 4 5 6 7 ... 34

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs141270051	chrX:6458485-6458486	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs182461274	chrX:6458559-6458560	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs375445575	chrX:6458733-6458734	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs555252906	chrX:6458831-6458832	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs145057916	chrX:6458864-6458865	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs372369109	chrX:6458883-6458884	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs187153004	chrX:6458918-6458919	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs377038209	chrX:6458992-6458993	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs138013896	chrX:6459020-6459021	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs369429636	chrX:6459074-6459075	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs192681605	chrX:6459093-6459094	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs182748291	chrX:6459102-6459103	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs188859486	chrX:6459155-6459156	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs193103974	chrX:6459176-6459177	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs184402558	chrX:6459288-6459289	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs187590787	chrX:6459348-6459349	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs567277707	chrX:6459463-6459464	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs192269217	chrX:6459571-6459572	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs66748526	chrX:6459580-6459581	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs189785100	chrX:6459702-6459703	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs35202738	chrX:6459790-6459791	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs550837231	chrX:6459904-6459905	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs373864258	chrX:6459905-6459906	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs180687762	chrX:6459980-6459981	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs141057176	chrX:6459990-6459991	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs3929647	chrX:6460019-6460020	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs150068086	chrX:6463757-6463758	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs368858044	chrX:6463808-6463809	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs372113359	chrX:6475046-6475047	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs191549604	chrX:6475131-6475132	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs112093599	chrX:6475142-6475143	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs142245777	chrX:6475284-6475285	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs187788622	chrX:6475432-6475433	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs111226258	chrX:6475453-6475454	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs369488757	chrX:6475468-6475469	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs112606519	chrX:6475517-6475518	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs5948736	chrX:6475629-6475630	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs200769113	chrX:6475659-6475660	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs182084037	chrX:6475662-6475663	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs186720829	chrX:6475679-6475680	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs113016559	chrX:6475820-6475821	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs191390599	chrX:6475825-6475826	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs7055580	chrX:6475897-6475898	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs11298425	chrX:6475909-6475910	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs200819088	chrX:6476180-6476181	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs4439307	chrX:6476202-6476203	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs185494766	chrX:6476224-6476225	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs190792196	chrX:6476225-6476226	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs148835904	chrX:6476269-6476270	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs4914914	chrX:6476350-6476351	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:65)

Disease	PMID	Source
turner syndrome	20877625	CNVD
Kallmann Syndrome 1	22470819	CNVD
short stature	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
Abnormal phenotypes	21355048	CNVD
Congenital abnormalities	21549014	CNVD
Developmental delay	21549014	CNVD
Mental retardation	21549014	CNVD
Microphthalmia	21572526	CNVD
Steroid sulfatase deficiency	21549014	CNVD
Attention deficit hyperactivity disorder	21355048	CNVD
Ichthyosis	21355048	CNVD
Mental retardation	21355048	CNVD
Immune disease	21076436	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
early-passage human iPS cells	21368824	CNVD
Developmental delay	21147756	CNVD
Epilepsy	22083797	CNVD
Bladder cancer	21909424	CNVD
Mental retardation	20877625	CNVD

Chromatin state (count:211 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:6458400-6460200	Enhancers	Dnd41	blood
2	chrX:6459200-6460000	Enhancers	Primary T cells from cord blood	blood
3	chrX:6463600-6464000	Enhancers	Fetal Thymus	thymus
4	chrX:6475000-6476600	Enhancers	Liver	Liver
5	chrX:6479000-6486000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chrX:6482400-6482600	Enhancers	Placenta	Placenta
7	chrX:6482600-6484800	Weak transcription	Placenta	Placenta
8	chrX:6483800-6484200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chrX:6484800-6486600	Enhancers	Placenta	Placenta
10	chrX:6486000-6486600	Enhancers	H9 Cell Line	embryonic stem cell
11	chrX:6494600-6499000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chrX:6499400-6499600	Enhancers	H9 Cell Line	embryonic stem cell
13	chrX:6506800-6508600	Enhancers	Dnd41	blood
14	chrX:6517000-6517800	Enhancers	Liver	Liver
15	chrX:6525200-6525400	Enhancers	H9 Cell Line	embryonic stem cell
16	chrX:6525400-6529600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chrX:6526200-6526600	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chrX:6532000-6532800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chrX:6532000-6532800	Enhancers	Fetal Brain Male	brain
20	chrX:6532000-6533600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chrX:6532200-6533200	Enhancers	Fetal Brain Female	brain
22	chrX:6548000-6548600	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chrX:6548000-6548600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chrX:6548000-6548800	Enhancers	Fetal Thymus	thymus
25	chrX:6560800-6561400	Enhancers	Dnd41	blood
26	chrX:6564400-6564800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chrX:6564600-6567000	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chrX:6573000-6573200	Enhancers	H9 Cell Line	embryonic stem cell
29	chrX:6573200-6574800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chrX:6573600-6575600	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chrX:6574400-6575600	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chrX:6575600-6576400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chrX:6576000-6576400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
34	chrX:6576000-6576600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
35	chrX:6577000-6583600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chrX:6577800-6580000	Enhancers	NHEK	skin
37	chrX:6578200-6578600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chrX:6578200-6579800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chrX:6578200-6580200	Enhancers	HMEC	breast
40	chrX:6578600-6579400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chrX:6579000-6579600	Enhancers	Dnd41	blood
42	chrX:6579400-6579600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chrX:6579600-6585400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chrX:6580200-6584400	Weak transcription	HMEC	breast
45	chrX:6580600-6580800	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chrX:6580800-6581400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chrX:6581400-6582000	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chrX:6581400-6582200	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chrX:6581600-6582200	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chrX:6582000-6582400	Enhancers	HUES48 Cell Line	embryonic stem cell

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