Variant report

Variant	nsv7116
Chromosome Location	chrX:138815720-138851105
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:138848644-138849177	GM12878	blood:	n/a	n/a
2	BACH1	chrX:138841786-138842138	H1-hESC	embryonic stem cell:	n/a	n/a
3	BATF	chrX:138821429-138821667	GM12878	blood:	n/a	chrX:138821643-138821651
4	BATF	chrX:138848899-138849232	GM12878	blood:	n/a	chrX:138849038-138849049
5	BATF	chrX:138848880-138849203	GM12878	blood:	n/a	chrX:138849038-138849049
6	BHLHE40	chrX:138821402-138821731	GM12878	blood:	n/a	n/a
7	BHLHE40	chrX:138848649-138849153	GM12878	blood:	n/a	n/a
8	CEBPB	chrX:138842808-138843002	A549	lung:	n/a	chrX:138842930-138842939
9	CEBPB	chrX:138842790-138843017	IMR90	lung:	n/a	chrX:138842930-138842939
10	CEBPB	chrX:138844670-138845040	IMR90	lung:	n/a	n/a
11	CHD2	chrX:138849187-138849211	GM12878	blood:	n/a	n/a
12	CREB1	chrX:138821435-138821749	GM12878	blood:	n/a	n/a
13	CTCF	chrX:138841880-138842030	HCT-116	colon:	n/a	n/a
14	CTCF	chrX:138841940-138842090	HRE	kidney:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
15	CTCF	chrX:138842000-138842150	GM12872	blood:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
16	CTCF	chrX:138841980-138842130	AG09319	gingival:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
17	CTCF	chrX:138841960-138842110	GM12873	blood:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
18	CTCF	chrX:138841911-138842164	MCF-7	breast:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
19	CTCF	chrX:138841880-138842030	GM12870	blood:	n/a	n/a
20	CTCF	chrX:138841940-138842090	A549	lung:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
21	CTCF	chrX:138841824-138842267	MCF-7	breast:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
22	CTCF	chrX:138841927-138842198	H1-hESC	embryonic stem cell:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
23	CTCF	chrX:138841912-138842170	K562	blood:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
24	CTCF	chrX:138841940-138842090	K562	blood:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
25	CTCF	chrX:138841960-138842110	HBMEC	blood vessel:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
26	CTCF	chrX:138842007-138842046	NHEK	skin:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
27	CTCF	chrX:138841960-138842110	HA-sp	spinal cord:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
28	CTCF	chrX:138841924-138842184	LNCaP	prostate:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
29	CTCF	chrX:138841960-138842110	HEEpiC	esophagus:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
30	CTCF	chrX:138841940-138842090	HMEC	breast:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
31	CTCF	chrX:138841940-138842090	Caco-2	colon:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
32	CTCF	chrX:138842020-138842170	AoAF	blood vessel:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
33	CTCF	chrX:138841980-138842130	GM12869	blood:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
34	CTCF	chrX:138841953-138842149	Spleen_OC	spleen:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
35	CTCF	chrX:138841833-138842238	K562	blood:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
36	CTCF	chrX:138841920-138842070	AG09319	gingival:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
37	CTCF	chrX:138841960-138842110	GM12864	blood:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
38	CTCF	chrX:138841980-138842130	HVMF	connective:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
39	CTCF	chrX:138841940-138842090	GM12864	blood:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
40	CTCF	chrX:138841920-138842070	NHEK	skin:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
41	CTCF	chrX:138841980-138842130	HCT-116	colon:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
42	CTCF	chrX:138841967-138842131	Kidney_OC	kidney:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
43	CTCF	chrX:138841960-138842110	HUVEC	blood vessel:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
44	CTCF	chrX:138841960-138842110	HVMF	connective:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
45	CTCF	chrX:138833374-138833421	ProgFib	skin:	n/a	n/a
46	CTCF	chrX:138841992-138842117	GM13976	blood:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
47	CTCF	chrX:138841954-138842069	HepG2	liver:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
48	CTCF	chrX:138841940-138842090	GM12875	blood:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
49	CTCF	chrX:138841920-138842070	SK-N-SH_RA	brain:	n/a	chrX:138842020-138842041 chrX:138842025-138842043
50	CTCF	chrX:138841846-138842244	IMR90	lung:	n/a	chrX:138842020-138842041 chrX:138842025-138842043

No.	Distal block	Cell Line	Cell type
1	chrX:138818456..138819998-chrX:138822453..138824439,2	MCF-7	breast:
2	chrX:138838803..138840480-chrX:139013697..139015277,2	K562	blood:
3	chrX:138818456..138819998-chrX:138822453..138824439,2	MCF-7	breast:
4	chrX:138825617..138827218-chrX:139013676..139015564,2	MCF-7	breast:
5	chrX:137838193..137839081-chrX:138841747..138842487,2	MCF-7	breast:
6	chrX:138796802..138798801-chrX:138817390..138820201,2	K562	blood:
7	chrX:138826048..138827648-chrX:138828172..138829873,2	MCF-7	breast:
8	chrX:138824358..138825919-chrX:139013684..139015708,2	K562	blood:
9	chrX:138826048..138827648-chrX:138828172..138829873,2	MCF-7	breast:
10	chrX:138816237..138818464-chrX:139013514..139016259,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MCF2-2	chrX:138842751-138842962	expReg_chrX_8519_-

Variant related genes	Relation type
ATP11C	TF binding region
ENSG00000101974	chromatin interactions

Extended variants
information (count: 465 )
Associated
traits (count: 45 )

Variant overlapped rSNPs/rCNVs (count:465 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs181327716	chrX:138815727-138815728	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs372796629	chrX:138816017-138816018	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs377171331	chrX:138816242-138816243	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs146601289	chrX:138816434-138816435	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs199579709	chrX:138816470-138816471	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs113893982	chrX:138816473-138816474	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs398073711	chrX:138816474-138816475	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs185200084	chrX:138816796-138816797	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs368280598	chrX:138816810-138816811	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs191137476	chrX:138816943-138816944	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs75387118	chrX:138817504-138817505	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs182028564	chrX:138817605-138817606	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs116061151	chrX:138817627-138817628	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs371975343	chrX:138817712-138817713	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs571404072	chrX:138817809-138817810	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs537457381	chrX:138817833-138817834	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs141611032	chrX:138817900-138817901	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs187670324	chrX:138817962-138817963	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs147038228	chrX:138817973-138817974	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs374577252	chrX:138817986-138817987	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs191977169	chrX:138818074-138818075	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs73634061	chrX:138818178-138818179	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs182743133	chrX:138818212-138818213	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs187440198	chrX:138818304-138818305	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs75820507	chrX:138818335-138818336	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs398102238	chrX:138818345-138818346	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs573895535	chrX:138818401-138818402	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs369235921	chrX:138818418-138818419	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs190007619	chrX:138818537-138818538	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs35823846	chrX:138818600-138818601	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs182639379	chrX:138818613-138818614	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs573348077	chrX:138818663-138818664	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs187552680	chrX:138818706-138818707	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs192792824	chrX:138818834-138818835	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs138117451	chrX:138818925-138818926	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs149653215	chrX:138819020-138819021	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs144386521	chrX:138819100-138819101	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs185534642	chrX:138819139-138819140	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs188857679	chrX:138819204-138819205	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs112405628	chrX:138819207-138819208	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs80143843	chrX:138819208-138819209	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs193103708	chrX:138819237-138819238	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs184402433	chrX:138819284-138819285	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs142121848	chrX:138819380-138819381	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs189156342	chrX:138819516-138819517	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs181180459	chrX:138819603-138819604	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs184290673	chrX:138819709-138819710	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs17328640	chrX:138819852-138819853	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
49	rs373706463	chrX:138819989-138819990	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs201858795	chrX:138820068-138820069	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:45)

Disease	PMID	Source
Neuroblastoma	18923191	CNVD
Burkitt''s lymphoma	20823134	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	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
Cancer	20581869	CNVD
Multiple myeloma	20724749	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Prostate cancer	18632612	CNVD
Lung cancer	18438408	CNVD
Autism	22495311	CNVD
lymphocytic leukemia	21291569	CNVD
Testicular germ cell tumor	18059402	CNVD
Testicular cancer	18059402	CNVD
Seminomas	18059402	CNVD
Glioblastoma multiforme	19960244	CNVD
Endometrial cancer	22040021	CNVD
Burkitt''s lymphoma	18698080	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	17387387	CNVD
Cancer	16751803	CNVD
small cell lung cancer	20016488	CNVD
Congenital Hypertrichosis Syndrome	21636067	CNVD
Congenital abnormalities	21549014	CNVD
Developmental delay	21549014	CNVD
Mental retardation	21549014	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Breast cancer	17603634	CNVD
abnormal development	18461090	CNVD
Multiple myeloma	17550852	CNVD
Premature ovarian failure	20952765	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Breast cancer	21364760	CNVD
Hereditary coagulopathy	21993689	CNVD
Cerebellar atrophy	21569638	CNVD
Fragile x	21569638	CNVD
Abnormal corpus callosum	21572526	CNVD
Congenital diaphragmatic hernia	21525063	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:493 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:138797000-138821000	Weak transcription	Primary T cells from cord blood	blood
2	chrX:138802200-138816200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chrX:138802200-138818800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chrX:138802200-138836600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chrX:138802400-138820800	Weak transcription	Hela-S3	cervix
6	chrX:138802400-138821800	Weak transcription	HSMM	muscle
7	chrX:138802600-138820400	Weak transcription	HUVEC	blood vessel
8	chrX:138803800-138821000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chrX:138804600-138817000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chrX:138804800-138832000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chrX:138805200-138829200	Weak transcription	Duodenum Mucosa	Duodenum
12	chrX:138805400-138819600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chrX:138805400-138835200	Weak transcription	Primary hematopoietic stem cells	blood
14	chrX:138805800-138820800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chrX:138806400-138819600	Weak transcription	Fetal Intestine Large	intestine
16	chrX:138806600-138836400	Weak transcription	Dnd41	blood
17	chrX:138806800-138820800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chrX:138806800-138866800	Weak transcription	Left Ventricle	heart
19	chrX:138807200-138858200	Weak transcription	Primary B cells from cord blood	blood
20	chrX:138807400-138817600	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chrX:138807600-138820800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chrX:138807600-138831200	Weak transcription	Fetal Muscle Trunk	muscle
23	chrX:138807800-138825400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chrX:138807800-138832400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chrX:138808200-138835600	Weak transcription	Fetal Stomach	stomach
26	chrX:138808400-138818000	Weak transcription	GM12878-XiMat	blood
27	chrX:138808400-138832600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chrX:138809000-138822600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chrX:138809000-138836000	Weak transcription	Adipose Nuclei	Adipose
30	chrX:138809600-138818600	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chrX:138810000-138818800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chrX:138810000-138827200	Weak transcription	Stomach Smooth Muscle	stomach
33	chrX:138810000-138835000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chrX:138810600-138820400	Weak transcription	HSMMtube	muscle
35	chrX:138810600-138840400	Weak transcription	K562	blood
36	chrX:138811200-138834800	Weak transcription	Spleen	Spleen
37	chrX:138811400-138822400	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chrX:138811800-138818800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chrX:138812200-138818000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chrX:138812200-138832200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chrX:138812600-138817600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chrX:138812800-138818600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chrX:138812800-138826000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chrX:138812800-138831200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chrX:138812800-138835600	Weak transcription	Fetal Thymus	thymus
46	chrX:138813600-138833400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chrX:138814000-138820800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chrX:138814000-138883600	Weak transcription	Gastric	stomach
49	chrX:138814200-138816200	Weak transcription	Liver	Liver
50	chrX:138814200-138848400	Weak transcription	H9 Cell Line	embryonic stem cell

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