Variant report

Variant	esv3441367
Chromosome Location	chrX:154906586-155188122
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	chrX:154996976-154997295	K562	blood:	n/a	n/a
2	ARID3A	chrX:154975527-154975836	K562	blood:	n/a	n/a
3	ATF2	chrX:155106295-155106691	GM12878	blood:	n/a	n/a
4	ATF2	chrX:155110700-155111118	GM12878	blood:	n/a	n/a
5	ATF3	chrX:155049878-155050047	K562	blood:	n/a	n/a
6	ATF3	chrX:155117896-155118116	K562	blood:	n/a	n/a
7	ATF3	chrX:155049810-155050080	H1-hESC	embryonic stem cell:	n/a	n/a
8	ATF3	chrX:155117821-155118206	K562	blood:	n/a	n/a
9	ATF3	chrX:155110793-155111031	K562	blood:	n/a	n/a
10	ATF3	chrX:155049846-155050087	K562	blood:	n/a	n/a
11	BCLAF1	chrX:155110613-155111149	GM12878	blood:	n/a	chrX:155111130-155111143
12	BCLAF1	chrX:155110620-155111034	GM12878	blood:	n/a	n/a
13	BHLHE40	chrX:154975442-154975772	K562	blood:	n/a	n/a
14	BHLHE40	chrX:154997079-154997133	K562	blood:	n/a	n/a
15	BHLHE40	chrX:154974371-154974416	K562	blood:	n/a	n/a
16	BRCA1	chrX:154907451-154907479	GM12878	blood:	n/a	n/a
17	BRCA1	chrX:154917275-154917410	Hela-S3	cervix:	n/a	n/a
18	BRCA1	chrX:154996864-154997304	Hela-S3	cervix:	n/a	n/a
19	CBX3	chrX:155097474-155097882	K562	blood:	n/a	n/a
20	CBX3	chrX:154970062-154970345	K562	blood:	n/a	n/a
21	CBX3	chrX:155110478-155111375	K562	blood:	n/a	n/a
22	CBX3	chrX:155157333-155157707	K562	blood:	n/a	n/a
23	CBX3	chrX:155097539-155097798	K562	blood:	n/a	n/a
24	CBX3	chrX:155117763-155118332	HCT-116	colon:	n/a	n/a
25	CBX3	chrX:155117729-155118210	HCT-116	colon:	n/a	n/a
26	CEBPB	chrX:155008478-155008899	MCF-7	breast:	n/a	n/a
27	CEBPB	chrX:154998078-154998477	A549	lung:	n/a	chrX:154998258-154998271 chrX:154998258-154998269
28	CEBPB	chrX:154977169-154977580	ECC-1	luminal epithelium:	n/a	n/a
29	CEBPB	chrX:154977178-154977591	Hela-S3	cervix:	n/a	n/a
30	CEBPB	chrX:154996507-154997170	Hela-S3	cervix:	n/a	n/a
31	CEBPB	chrX:154959881-154960167	A549	lung:	n/a	n/a
32	CEBPB	chrX:154977314-154977417	K562	blood:	n/a	n/a
33	CEBPB	chrX:154998121-154998506	MCF-7	breast:	n/a	chrX:154998258-154998271 chrX:154998258-154998269
34	CEBPB	chrX:154975317-154975850	Hela-S3	cervix:	n/a	n/a
35	CEBPB	chrX:154998099-154998478	IMR90	lung:	n/a	chrX:154998258-154998271 chrX:154998258-154998269
36	CEBPB	chrX:154998136-154998445	HepG2	liver:	n/a	chrX:154998258-154998271 chrX:154998258-154998269
37	CEBPB	chrX:154977282-154977613	ECC-1	luminal epithelium:	n/a	n/a
38	CEBPB	chrX:154998108-154998472	Hela-S3	cervix:	n/a	chrX:154998258-154998271 chrX:154998258-154998269
39	CEBPB	chrX:155008503-155008956	MCF-7	breast:	n/a	n/a
40	CEBPB	chrX:155049796-155050155	MCF-7	breast:	n/a	n/a
41	CEBPB	chrX:154996928-154997103	IMR90	lung:	n/a	n/a
42	CEBPD	chrX:155110955-155111174	HepG2	liver:	n/a	n/a
43	CHD2	chrX:154996956-154997273	K562	blood:	n/a	n/a
44	CHD2	chrX:154975613-154975743	K562	blood:	n/a	n/a
45	CHD2	chrX:154996669-154997437	Hela-S3	cervix:	n/a	chrX:154996886-154996896
46	CHD2	chrX:154997004-154997475	H1-hESC	embryonic stem cell:	n/a	n/a
47	CREB1	chrX:155110547-155111661	HepG2	liver:	n/a	chrX:155111461-155111474
48	CREB1	chrX:155110712-155111544	HepG2	liver:	n/a	chrX:155111461-155111474
49	CREB1	chrX:155110727-155111073	A549	lung:	n/a	n/a
50	CREB1	chrX:155110556-155111675	K562	blood:	n/a	chrX:155111461-155111474

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:154899237..154900918-chrX:154908592..154911481,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VAMP7-2	chrX:155105299-155105548	NONHSAT139247
2	lnc-TMLHE-3	chrX:155058248-155059239	NONHSAT139246

No.	miRNA target gene	miRNA name	Chromosome Location
1	VAMP7	hsa-miR-26b-5p	chrX:155172667-155172687
2	SPRY3	hsa-miR-320a	chrX:155004589-155004612
3	VAMP7	hsa-miR-1	chrX:155173195-155173215
4	VAMP7	hsa-miR-93-5p	chrX:155172890-155172912

Variant related genes	Relation type
AMDP1	TF binding region
VAMP7	TF binding region
SPRY3	TF binding region
DPH3P2	TF binding region
ENSG00000185973	chromatin interactions

Extended variants
information (count: 2420 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:2420 , 50 per page) page: 1 2 3 4 5 6 7 ... 49

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs189626042	chrX:154908701-154908702	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs601837	chrX:154908749-154908750	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs140637334	chrX:154908839-154908840	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs601343	chrX:154908908-154908909	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs372186142	chrX:154908940-154908941	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs473529	chrX:154909055-154909056	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs192263848	chrX:154909077-154909078	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs202076015	chrX:154909106-154909107	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs184283223	chrX:154909125-154909126	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs188773260	chrX:154909216-154909217	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs181126865	chrX:154909374-154909375	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs73562831	chrX:154909434-154909435	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs138278793	chrX:154909441-154909442	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs188877959	chrX:154909522-154909523	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs368834020	chrX:154909604-154909605	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs182584986	chrX:154909691-154909692	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs61602599	chrX:154909852-154909853	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs586456	chrX:154909875-154909876	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs586454	chrX:154909877-154909878	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs112839770	chrX:154909888-154909889	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs373341470	chrX:154909893-154909894	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs372622256	chrX:154909985-154909986	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs187148778	chrX:154910041-154910042	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs191158258	chrX:154910071-154910072	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs182481016	chrX:154910142-154910143	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs150238120	chrX:154910537-154910538	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs138966106	chrX:154910547-154910548	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs78454675	chrX:154910556-154910557	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs184968614	chrX:154910558-154910559	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs368231076	chrX:154910576-154910577	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs34516829	chrX:154910630-154910631	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs190142529	chrX:154910646-154910647	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs147364233	chrX:154910802-154910803	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs182378404	chrX:154910859-154910860	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs187532185	chrX:154910943-154910944	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs7473652	chrX:154910996-154910997	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs199805039	chrX:154911033-154911034	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs375013532	chrX:154911047-154911048	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs6642309	chrX:154911142-154911143	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs137909472	chrX:154911196-154911197	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs143374625	chrX:154911237-154911238	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs191547453	chrX:154911273-154911274	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs184193051	chrX:154911415-154911416	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs3905538	chrX:154916435-154916436	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs183209508	chrX:154916512-154916513	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs186964321	chrX:154916809-154916810	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs375562221	chrX:154916835-154916836	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs669237	chrX:154916845-154916846	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs369489556	chrX:154916869-154916870	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs145742782	chrX:154916986-154916987	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:64)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
Astrocytoma	17387387	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Metanephric adenoma	20802469	CNVD
Medulloblastoma	21979893	CNVD
Schizophrenia	23904455	CNVD
Olfactory neuroblastoma	18408657	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
Congenital abnormalities	21549014	CNVD
Developmental delay	21549014	CNVD
Mental retardation	21549014	CNVD
Premature ovarian failure	20952765	CNVD
Abnormal corpus callosum	21572526	CNVD
Breast cancer	21364760	CNVD
Astrocytoma	22246337	CNVD
Cerebellar atrophy	21569638	CNVD
periventricular nodular heterotopia	21572526	CNVD
Cerebellar hypoplasia	21569638	CNVD
Hoyeraal-Hreidarsson syndrome	21569638	CNVD
Oto-palato-digital type II	21569638	CNVD
incontinentia pigmenti anhidrotic ectodermal dysplasia with immunodeficiency	18350553	CNVD
Aqueductal stenosis	21572526	CNVD
Hirschsprung''s Disease	21712996	CNVD
Vermis hypoplasia	21569638	CNVD
X-linked hydrocephalus	21569638	CNVD
Rett syndrome	21569638	CNVD
Austim spectrum disorder	21302340	CNVD
Autism	20970697	CNVD
Epilepsy	20970697	CNVD
Hemophilia A	17823971	CNVD
Rett syndrome	18923514	CNVD
Rett syndrome	22241247	CNVD
Intellectual disability	21984752	CNVD
Mental retardation	19951919	CNVD
Hypotonia	17088400	CNVD
Intellectual disability	22511893	CNVD
Mental retardation	17088400	CNVD
Mental retardation	21119712	CNVD
Neurodevelopmental disorder	19324899	CNVD
Recurrent Infections	17088400	CNVD
Rett syndrome	22283845	CNVD
Rett syndrome	21383316	CNVD
Cryptorchidism	21048976	CNVD
Disorders of sex development	21048976	CNVD
Cervical cancer	21062161	CNVD
Congenital Hypertrichosis Syndrome	21636067	CNVD
Hemophilia A	18787571	CNVD
Hunters syndrom	18787571	CNVD
Prader-willi syndrome	20588305	CNVD
Mental retardation	19057379	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
abortions and stillbirths	19751515	CNVD
Intellectual disability	23615299	CNVD
Lung cancer	18438408	CNVD
small cell lung cancer	20016488	CNVD

Chromatin state (count:2115 , 50 per page) page: 1 2 3 4 5 6 7 ... 43

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:154909000-154909400	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chrX:154916400-154917000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chrX:154917000-154917600	Enhancers	Hela-S3	cervix
4	chrX:154944400-154945400	Enhancers	NHEK	skin
5	chrX:154944600-154945600	Enhancers	Hela-S3	cervix
6	chrX:154944600-154945800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chrX:154944800-154945600	Enhancers	Fetal Thymus	thymus
8	chrX:154947400-154947600	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chrX:154948400-154948800	Active TSS	Skeletal Muscle Male	skeletal muscle
10	chrX:154948400-154948800	Active TSS	Skeletal Muscle Female	skeletal muscle
11	chrX:154948400-154949200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chrX:154948400-154949200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chrX:154948400-154949200	Enhancers	Stomach Smooth Muscle	stomach
14	chrX:154948400-154949400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chrX:154948600-154949000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chrX:154948600-154949000	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chrX:154948600-154949200	Enhancers	HSMMtube	muscle
18	chrX:154948600-154949600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chrX:154948600-154950200	Enhancers	Right Ventricle	heart
20	chrX:154948800-154949000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chrX:154948800-154949200	Enhancers	Fetal Heart	heart
22	chrX:154948800-154949200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chrX:154948800-154949400	Enhancers	Primary B cells from peripheral blood	blood
24	chrX:154948800-154949400	Enhancers	Aorta	Aorta
25	chrX:154948800-154949600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chrX:154948800-154949600	Enhancers	Left Ventricle	heart
27	chrX:154949000-154949200	Active TSS	Skeletal Muscle Male	skeletal muscle
28	chrX:154949200-154949400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chrX:154949200-154949600	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chrX:154949400-154949600	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chrX:154958000-154958400	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chrX:154958200-154958400	Enhancers	Gastric	stomach
33	chrX:154961000-154962600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chrX:154961000-154962600	Active TSS	Ovary	ovary
35	chrX:154961200-154962200	Active TSS	Aorta	Aorta
36	chrX:154961400-154961800	Active TSS	Adipose Nuclei	Adipose
37	chrX:154961400-154961800	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chrX:154961400-154962000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chrX:154961400-154962000	Active TSS	Right Atrium	heart
40	chrX:154962000-154962200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chrX:154962200-154962400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chrX:154962200-154962600	Enhancers	Fetal Heart	heart
43	chrX:154962200-154963200	Weak transcription	Aorta	Aorta
44	chrX:154962400-154962600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chrX:154963200-154963400	Enhancers	Aorta	Aorta
46	chrX:154963400-154963800	Enhancers	Stomach Mucosa	stomach
47	chrX:154963400-154964000	Weak transcription	Aorta	Aorta
48	chrX:154963600-154964000	Enhancers	H1 Cell Line	embryonic stem cell
49	chrX:154969000-154973000	Weak transcription	Psoas Muscle	Psoas
50	chrX:154969000-154974000	Weak transcription	Aorta	Aorta

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