Variant report

Variant	rs6539173
Chromosome Location	chr12:105358315-105358316
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10861300	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11112268	0.97[ASN][1000 genomes]
rs11112269	0.97[ASN][1000 genomes]
rs12230563	1.00[ASN][1000 genomes]
rs4310692	0.83[EUR][1000 genomes]
rs4964119	0.83[EUR][1000 genomes]
rs4964309	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4964318	0.80[EUR][1000 genomes]
rs6539174	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6539178	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6539179	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6539180	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7138144	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7299739	0.83[EUR][1000 genomes]
rs7307234	0.87[ASN][1000 genomes]

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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105353800-105358800	Weak transcription	GM12878-XiMat	blood
2	chr12:105356600-105359400	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr12:105357000-105358800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:105357400-105358800	Enhancers	Fetal Brain Male	brain
5	chr12:105357400-105359000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:105358000-105358400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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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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