Variant report

Variant	rs1462777
Chromosome Location	chr4:98238605-98238606
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10213433	0.83[EUR][1000 genomes]
rs1841792	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28519591	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28539905	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28571811	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6823738	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72881915	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7655672	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7680213	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7680402	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879640	chr4:97711707-98697586	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv830014	chr4:98220259-98419635	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:98237800-98239800	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr4:98238200-98239800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:98238200-98239800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr4:98238200-98239800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr4:98238200-98240000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:98238200-98240000	Enhancers	Brain Germinal Matrix	brain
7	chr4:98238400-98239000	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr4:98238400-98239600	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr4:98238400-98239800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:98238600-98238800	Enhancers	Liver	Liver
11	chr4:98238600-98239000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr4:98238600-98239000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr4:98238600-98239200	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr4:98238600-98239600	Weak transcription	Fetal Brain Male	brain
15	chr4:98238600-98240000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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

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