Variant report

Variant	rs12611593
Chromosome Location	chr2:125332674-125332675
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12613338	0.98[ASN][1000 genomes]
rs12613738	0.82[CHB][hapmap]
rs12618039	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs12618822	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12621453	1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs13430312	0.82[CHB][hapmap]
rs1542918	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17011732	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17320347	1.00[CHB][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs2901331	1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs34420072	0.86[ASN][1000 genomes]
rs35151213	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36064320	0.86[ASN][1000 genomes]
rs6737746	0.82[CHB][hapmap]
rs6739605	1.00[CHB][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs7420022	0.86[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs7601703	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs7601825	0.85[CHB][hapmap];0.83[CHD][hapmap]

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	nsv1014610	chr2:125124983-125350342	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv834357	chr2:125258157-125421507	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12611593	LHFP	trans	lymphoblastoid	seeQTL
rs12611593	ARHGAP20	trans	lymphoblastoid	seeQTL
rs12611593	FHL1	trans	lymphoblastoid	seeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:125321600-125345200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:125329000-125333000	Weak transcription	Liver	Liver
3	chr2:125331800-125333200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:125332000-125335200	Weak transcription	HepG2	liver

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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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