Variant report

Variant	esv2755043
Chromosome Location	chrX:6482092-6674211
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:6656521-6657470	GM12878	blood:	n/a	n/a
2	ATF2	chrX:6656510-6657531	GM12878	blood:	n/a	n/a
3	ATF2	chrX:6650200-6650576	GM12878	blood:	n/a	n/a
4	BATF	chrX:6656848-6657191	GM12878	blood:	n/a	n/a
5	BATF	chrX:6656817-6657350	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:6650178-6650508	GM12878	blood:	n/a	n/a
11	BCLAF1	chrX:6656899-6657442	GM12878	blood:	n/a	n/a
12	BCLAF1	chrX:6656774-6657546	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	BHLHE40	chrX:6666733-6666965	GM12878	blood:	n/a	n/a
16	BRCA1	chrX:6656940-6657436	GM12878	blood:	n/a	n/a
17	CEBPB	chrX:6584778-6584931	A549	lung:	n/a	n/a
18	CEBPB	chrX:6524963-6525194	IMR90	lung:	n/a	chrX:6525062-6525075
19	CEBPB	chrX:6670703-6670928	HepG2	liver:	n/a	chrX:6670833-6670844 chrX:6670846-6670857 chrX:6670832-6670845
20	CEBPB	chrX:6656583-6657408	GM12878	blood:	n/a	n/a
21	CEBPB	chrX:6524895-6525228	A549	lung:	n/a	chrX:6525062-6525075
22	CEBPB	chrX:6648377-6648623	IMR90	lung:	n/a	chrX:6648460-6648469 chrX:6648460-6648471
23	CEBPB	chrX:6670704-6670919	Hela-S3	cervix:	n/a	chrX:6670833-6670844 chrX:6670846-6670857 chrX:6670832-6670845
24	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
25	CEBPB	chrX:6636479-6636630	K562	blood:	n/a	chrX:6636549-6636560
26	CEBPB	chrX:6636405-6636717	A549	lung:	n/a	chrX:6636549-6636560
27	CEBPB	chrX:6636401-6636732	IMR90	lung:	n/a	chrX:6636549-6636560
28	CEBPB	chrX:6636411-6636698	HepG2	liver:	n/a	chrX:6636549-6636560
29	CEBPB	chrX:6555739-6556013	IMR90	lung:	n/a	chrX:6555877-6555888
30	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
31	CEBPB	chrX:6648360-6648619	HepG2	liver:	n/a	chrX:6648460-6648469 chrX:6648460-6648471
32	CEBPB	chrX:6670723-6670987	IMR90	lung:	n/a	chrX:6670833-6670844 chrX:6670846-6670857 chrX:6670832-6670845
33	CEBPB	chrX:6670740-6670985	A549	lung:	n/a	chrX:6670833-6670844 chrX:6670846-6670857 chrX:6670832-6670845
34	CEBPB	chrX:6555794-6556010	HepG2	liver:	n/a	chrX:6555877-6555888
35	CEBPB	chrX:6484827-6485100	IMR90	lung:	n/a	n/a
36	CEBPB	chrX:6584701-6584981	IMR90	lung:	n/a	n/a
37	CEBPD	chrX:6622445-6623267	K562	blood:	n/a	n/a
38	CHD1	chrX:6666908-6666979	GM12878	blood:	n/a	n/a
39	CHD1	chrX:6656661-6657832	GM12878	blood:	n/a	n/a
40	CHD1	chrX:6656382-6656383	GM12878	blood:	n/a	n/a
41	CHD2	chrX:6611235-6611270	H1-hESC	embryonic stem cell:	n/a	n/a
42	CHD2	chrX:6650219-6650419	GM12878	blood:	n/a	n/a
43	CHD2	chrX:6666762-6666938	GM12878	blood:	n/a	n/a
44	CHD2	chrX:6656289-6657671	GM12878	blood:	n/a	n/a
45	CTCF	chrX:6616573-6616600	LNCaP	prostate:	n/a	n/a
46	CTCF	chrX:6562554-6562611	MCF-7	breast:	n/a	n/a
47	CTCF	chrX:6562520-6562670	GM12873	blood:	n/a	n/a
48	CTCF	chrX:6548359-6548430	GM10248	blood:	n/a	n/a
49	CTCF	chrX:6562512-6562804	GM12878	blood:	n/a	n/a
50	CTCF	chrX:6562520-6562670	GM12864	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:6634384-6634507	NONHSAT136173
2	lnc-VCX3A-2	chrX:6649458-6649585	NONHSAT136173
3	lnc-VCX3A-2	chrX:6595906-6596170	NONHSAT136173

Variant related genes	Relation type
ENSG00000231217	TF binding region

Extended variants
information (count: 1876 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:1876 , 50 per page) page: 1 2 3 4 5 6 7 ... 38

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs5948735	chrX:6482092-6482093	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs181673621	chrX:6482096-6482097	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs185453172	chrX:6482145-6482146	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs199893248	chrX:6482168-6482169	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs368189521	chrX:6482171-6482172	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs150920541	chrX:6482180-6482181	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs140842038	chrX:6482188-6482189	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs556222988	chrX:6482209-6482210	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs6639643	chrX:6482210-6482211	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs61638818	chrX:6482212-6482213	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs565684290	chrX:6482255-6482256	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs191429543	chrX:6482514-6482515	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs182437082	chrX:6482522-6482523	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs374822232	chrX:6482543-6482544	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs187959236	chrX:6482589-6482590	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs200474158	chrX:6482775-6482776	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs554567297	chrX:6482988-6482989	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs35053316	chrX:6483034-6483035	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs140656773	chrX:6483135-6483136	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs190891414	chrX:6483325-6483326	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs183318377	chrX:6483340-6483341	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs188062787	chrX:6483420-6483421	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs192154597	chrX:6483468-6483469	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs150447223	chrX:6483522-6483523	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs184553079	chrX:6483528-6483529	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs3935013	chrX:6483529-6483530	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs187027451	chrX:6483603-6483604	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs192939729	chrX:6483732-6483733	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs184192043	chrX:6483798-6483799	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs67550276	chrX:6483821-6483822	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs189358634	chrX:6483852-6483853	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs181004076	chrX:6483955-6483956	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs113615894	chrX:6483958-6483959	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs189508922	chrX:6484106-6484107	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs143399996	chrX:6484142-6484143	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs139029235	chrX:6484206-6484207	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs66767837	chrX:6484320-6484321	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs115319260	chrX:6484325-6484326	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs111854547	chrX:6484443-6484444	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs181369844	chrX:6484504-6484505	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs150758913	chrX:6484590-6484591	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs372283135	chrX:6484660-6484661	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs113408357	chrX:6484677-6484678	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs61175923	chrX:6484678-6484679	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs572951170	chrX:6484718-6484719	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs377648006	chrX:6484731-6484732	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs540213051	chrX:6484784-6484785	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs185899652	chrX:6484877-6484878	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs370970913	chrX:6484995-6484996	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs74953156	chrX:6485035-6485036	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:64)

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
Developmental delay	21147756	CNVD
Epilepsy	22083797	CNVD
Bladder cancer	21909424	CNVD
Mental retardation	20877625	CNVD

Chromatin state (count:217 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:6479000-6486000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chrX:6482400-6482600	Enhancers	Placenta	Placenta
3	chrX:6482600-6484800	Weak transcription	Placenta	Placenta
4	chrX:6483800-6484200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chrX:6484800-6486600	Enhancers	Placenta	Placenta
6	chrX:6486000-6486600	Enhancers	H9 Cell Line	embryonic stem cell
7	chrX:6494600-6499000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chrX:6499400-6499600	Enhancers	H9 Cell Line	embryonic stem cell
9	chrX:6506800-6508600	Enhancers	Dnd41	blood
10	chrX:6517000-6517800	Enhancers	Liver	Liver
11	chrX:6525200-6525400	Enhancers	H9 Cell Line	embryonic stem cell
12	chrX:6525400-6529600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chrX:6526200-6526600	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chrX:6532000-6532800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chrX:6532000-6532800	Enhancers	Fetal Brain Male	brain
16	chrX:6532000-6533600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chrX:6532200-6533200	Enhancers	Fetal Brain Female	brain
18	chrX:6548000-6548600	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chrX:6548000-6548600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chrX:6548000-6548800	Enhancers	Fetal Thymus	thymus
21	chrX:6560800-6561400	Enhancers	Dnd41	blood
22	chrX:6564400-6564800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chrX:6564600-6567000	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chrX:6573000-6573200	Enhancers	H9 Cell Line	embryonic stem cell
25	chrX:6573200-6574800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chrX:6573600-6575600	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chrX:6574400-6575600	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chrX:6575600-6576400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chrX:6576000-6576400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
30	chrX:6576000-6576600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
31	chrX:6577000-6583600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chrX:6577800-6580000	Enhancers	NHEK	skin
33	chrX:6578200-6578600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chrX:6578200-6579800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chrX:6578200-6580200	Enhancers	HMEC	breast
36	chrX:6578600-6579400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chrX:6579000-6579600	Enhancers	Dnd41	blood
38	chrX:6579400-6579600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chrX:6579600-6585400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chrX:6580200-6584400	Weak transcription	HMEC	breast
41	chrX:6580600-6580800	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chrX:6580800-6581400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chrX:6581400-6582000	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chrX:6581400-6582200	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chrX:6581600-6582200	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chrX:6582000-6582400	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chrX:6582000-6583000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chrX:6582200-6583800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chrX:6583000-6583200	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chrX:6583600-6583800	Enhancers	H9 Cell Line	embryonic stem cell

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