Variant report

Variant	esv988822
Chromosome Location	chrX:5824938-5825500
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	POLR2A	chrX:5825272-5825642	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chrX:5824906-5825113	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chrX:5825449-5825675	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chrX:5825373-5825937	SK-N-MC	brain:	n/a	n/a
5	SIN3A	chrX:5825309-5825551	H1-hESC	embryonic stem cell:	n/a	n/a
6	TCF12	chrX:5825223-5825557	H1-hESC	embryonic stem cell:	n/a	chrX:5825430-5825440 chrX:5825327-5825335
7	TEAD4	chrX:5825203-5825496	H1-hESC	embryonic stem cell:	n/a	n/a
8	TEAD4	chrX:5825260-5825542	H1-hESC	embryonic stem cell:	n/a	n/a
9	ZNF143	chrX:5825205-5825445	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
NLGN4X	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 53 )

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs5916270	chrX:5824961-5824962	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs191693935	chrX:5824993-5824994	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs184251692	chrX:5824994-5824995	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs188147565	chrX:5825003-5825004	Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs191460934	chrX:5825009-5825010	Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs184731462	chrX:5825059-5825060	Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs199659684	chrX:5825133-5825134	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs6529896	chrX:5825331-5825332	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs144552825	chrX:5825462-5825463	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:53)

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
Pancreatic cancer	17952125	CNVD
Autism	20643418	CNVD
Autism	23710042	CNVD
Schizophrenia	23710042	CNVD

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:5799600-5828600	Weak transcription	Ovary	ovary
2	chrX:5806800-5833200	Strong transcription	Dnd41	blood
3	chrX:5817600-5825000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
4	chrX:5818800-5827000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chrX:5819200-5825600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chrX:5821200-5825400	Weak transcription	Brain Germinal Matrix	brain
7	chrX:5821200-5828400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chrX:5821200-5831200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chrX:5821800-5828200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chrX:5822200-5831200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chrX:5822600-5826200	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chrX:5822600-5828600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chrX:5823400-5826600	Strong transcription	Fetal Thymus	thymus
14	chrX:5823800-5825000	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chrX:5824400-5825400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chrX:5824400-5829400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chrX:5824800-5828800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chrX:5825000-5825800	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
19	chrX:5825000-5826000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
20	chrX:5825200-5826200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
21	chrX:5825400-5825600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chrX:5825400-5825800	Enhancers	HUES64 Cell Line	embryonic stem cell

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