Variant report

Variant	rs542609
Chromosome Location	chr9:25928440-25928441
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1219939	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1219941	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1219942	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs542788	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs562342	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs636294	0.87[EUR][1000 genomes]
rs644506	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs658858	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs861359	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015883	chr9:25633359-26315286	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1028267	chr9:25749378-25930340	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv892839	chr9:25750661-26050209	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2422440	chr9:25850788-25988298	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv892840	chr9:25867219-26034314	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv892841	chr9:25901396-25971497	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv466322	chr9:25904637-25934932	Enhancers Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
8	nsv613919	chr9:25904637-25934932	Enhancers Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
9	nsv1017295	chr9:25916353-26001315	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv466323	chr9:25919851-25971497	Flanking Active TSS Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv613920	chr9:25919851-25971497	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv471292	chr9:25919851-25988972	Weak transcription Flanking Active TSS Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv519537	chr9:25924754-25929109	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
14	nsv522142	chr9:25924754-25934932	Enhancers Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:25926800-25928600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr9:25926800-25929200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

Quick Search:

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

what's new

Quick links