Variant report

Variant	rs1417405
Chromosome Location	chr1:76457797-76457798
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10518521	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10782602	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10873787	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873788	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873808	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161845	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118399	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1689275	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17650138	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770885	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770887	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029683	1.00[ASN][1000 genomes]
rs4949683	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949686	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61770550	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61770556	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61770557	1.00[ASN][1000 genomes]
rs931507	0.80[EUR][1000 genomes];1.00[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	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1417405	MSH4	cis	Artery Tibial	GTEx
rs1417405	MSH4	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76457200-76457800	Enhancers	Brain Hippocampus Middle	brain
2	chr1:76457600-76458000	Enhancers	HUES64 Cell Line	embryonic stem cell

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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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