Variant report

Variant	rs12754425
Chromosome Location	chr1:179387109-179387110
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:18)

rs_ID	r²[population]
rs10913756	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10913765	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11580135	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11802595	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12729906	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12749731	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12752024	0.89[ASN][1000 genomes]
rs4424468	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4618931	0.85[ASN][1000 genomes]
rs4651031	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4651032	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4651033	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6425542	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6425543	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6425556	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6664339	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6690348	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6693627	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv548279	chr1:179323919-179390148	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
2	esv3514400	chr1:179349344-179400533	Enhancers Active TSS ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv3514401	chr1:179349344-179400533	Weak transcription Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv3451112	chr1:179352344-179400533	Enhancers ZNF genes & repeats Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv1819329	chr1:179371973-179442337	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv466217	chr1:179371973-179477921	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv548297	chr1:179371973-179477921	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv548298	chr1:179376896-179436288	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179387000-179389000	Weak transcription	hESC Derived CD184+ Endoderm 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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