Variant report

Variant	rs10506646
Chromosome Location	chr12:72396492-72396493
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1023989	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1023990	0.94[CEU][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10506645	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10748190	1.00[JPT][hapmap]
rs10879350	0.85[ASW][hapmap];0.84[CEU][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs10879352	1.00[JPT][hapmap]
rs11179002	0.88[CEU][hapmap]
rs11179023	1.00[CEU][hapmap];0.83[GIH][hapmap]
rs11179027	0.84[CEU][hapmap]
rs11179033	0.89[CEU][hapmap]
rs11179034	0.81[EUR][1000 genomes]
rs11834097	0.81[EUR][1000 genomes]
rs11834114	0.85[ASW][hapmap];0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs12229394	0.85[ASW][hapmap];0.84[CEU][hapmap];0.81[YRI][hapmap]
rs12319219	0.84[CEU][hapmap]
rs1386491	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1487278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17110477	0.88[CEU][hapmap]
rs17110489	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs17110532	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17110536	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17110540	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17110627	1.00[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs17110690	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2129576	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3903502	1.00[JPT][hapmap]
rs55851729	0.81[EUR][1000 genomes]
rs57706328	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59895192	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60032326	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73142538	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73142553	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73144406	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73144416	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9325202	0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048478	chr12:72145703-72401712	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv541530	chr12:72145703-72401712	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv518498	chr12:72307616-72508779	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1054578	chr12:72307616-72509341	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10506646	PYCS	trans	multi-tissue	Pritchard

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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