Variant report

Variant	rs2897242
Chromosome Location	chr5:2202272-2202273
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11133934	0.83[EUR][1000 genomes]
rs11958412	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12652348	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12653402	1.00[AFR][1000 genomes]
rs12655975	1.00[AFR][1000 genomes]
rs12658255	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12658661	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12658676	1.00[AFR][1000 genomes]
rs12659152	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16903506	1.00[AFR][1000 genomes]
rs16903516	1.00[AFR][1000 genomes]
rs16903550	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16903554	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16903629	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4262114	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs59236397	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60785554	1.00[AFR][1000 genomes]
rs67836064	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72491354	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
2	nsv880947	chr5:2146761-2251313	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv881232	chr5:2150273-2213762	ZNF genes & repeats Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv880789	chr5:2159490-2213762	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv596908	chr5:2186956-2254295	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv2568273	chr5:2202272-2202272	Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
7	esv2159446	chr5:2202272-2202273	Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:2201400-2203000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:2201400-2203000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:2201400-2205800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:2201400-2207800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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