Variant report

Variant	rs5762541
Chromosome Location	chr22:28666961-28666962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs17502181	0.81[CEU][hapmap]
rs2346395	0.85[CEU][hapmap]
rs5752710	0.87[ASW][hapmap]
rs5762532	0.87[ASW][hapmap];0.87[YRI][hapmap]
rs9613574	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv459866	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv588879	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5762541	RGL4	cis	parietal	SCAN
rs5762541	KIAA1671	cis	cerebellum	SCAN
rs5762541	TTC28	cis	cerebellum	SCAN
rs5762541	PITPNB	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28651800-28690600	Weak transcription	Dnd41	blood
2	chr22:28653000-28671600	Weak transcription	Fetal Stomach	stomach
3	chr22:28657000-28691600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr22:28659400-28671200	Weak transcription	Fetal Lung	lung
5	chr22:28662800-28671200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr22:28662800-28671200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr22:28663000-28671000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr22:28664400-28671800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr22:28664400-28674800	Weak transcription	NHDF-Ad	bronchial
10	chr22:28665200-28671000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr22:28665600-28677600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr22:28666200-28691000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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