Variant report

Variant	rs4858134
Chromosome Location	chr3:25006659-25006660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11129173	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12487571	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12490559	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12490596	0.82[EUR][1000 genomes]
rs13068239	0.81[EUR][1000 genomes]
rs28532700	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4075413	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4356783	0.82[EUR][1000 genomes]
rs4510351	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4858135	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4858671	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4858672	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62230582	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6768850	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7651592	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9825544	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9838340	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9849459	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9880826	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876630	chr3:24911917-25066711	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv834644	chr3:24936987-25112610	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv460482	chr3:24966768-25071616	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv589954	chr3:24966768-25071616	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv589955	chr3:24987823-25113358	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4858134	NKIRAS1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24996000-25007800	Weak transcription	Fetal Kidney	kidney
2	chr3:25005800-25006800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:25005800-25006800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:25006000-25007000	Weak transcription	A549	lung
5	chr3:25006000-25007600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:25006400-25006800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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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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