Variant report

Variant	rs2647125
Chromosome Location	chr4:125949982-125949983
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10009302	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10017393	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10025227	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10033725	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12646199	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12648351	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2647127	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2647129	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28434449	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56053689	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6534459	0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001338	chr4:125708756-126103293	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2647125	SLC47A2	trans	brain	seeQTL
rs2647125	KIF1C	trans	brain	seeQTL
rs2647125	LTF	trans	brain	seeQTL
rs2647125	CAPS	trans	brain	seeQTL
rs2647125	ANKRD40	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:125949400-125951400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:125949800-125950400	Enhancers	H9 Derived Neuron 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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