Variant report

Variant	rs6701520
Chromosome Location	chr1:73940718-73940719
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10789373	0.83[ASN][1000 genomes]
rs11210261	0.97[ASN][1000 genomes]
rs11210263	0.97[ASN][1000 genomes]
rs11210274	0.83[ASN][1000 genomes]
rs12026485	0.83[ASN][1000 genomes]
rs12754690	0.97[ASN][1000 genomes]
rs1923201	0.82[JPT][hapmap]
rs2341392	0.83[ASN][1000 genomes]
rs4113049	0.93[ASN][1000 genomes]
rs525701	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61605983	0.83[ASN][1000 genomes]
rs6698993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005356	chr1:73542786-74124065	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv870536	chr1:73647909-74031554	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6701520	MSH4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:73938600-73943200	Weak transcription	H1 BMP4 Derived Mesendoderm 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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