Variant report

Variant	rs17103342
Chromosome Location	chr1:47966860-47966861
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1024108	0.86[EUR][1000 genomes]
rs11585530	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588699	0.92[ASN][1000 genomes]
rs11590531	0.85[ASN][1000 genomes]
rs11799997	0.86[EUR][1000 genomes]
rs12065137	1.00[CHB][hapmap]
rs1415540	0.82[YRI][hapmap]
rs17103322	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17103383	0.86[EUR][1000 genomes]
rs2102437	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28493519	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471608	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478526	0.86[EUR][1000 genomes]
rs560540	0.86[EUR][1000 genomes]
rs56404532	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs578335	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59326446	0.91[EUR][1000 genomes]
rs59865928	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60503680	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs635710	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681140	0.83[EUR][1000 genomes]
rs6688849	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691723	1.00[CHB][hapmap]
rs72904553	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72904554	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531586	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7543243	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs822886	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][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	nsv1001779	chr1:47884229-48111485	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv871299	chr1:47889417-48057890	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	esv2755190	chr1:47907580-48048680	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17103342	MAST2	cis	cerebellum	SCAN
rs17103342	CDKN2C	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47961400-47968800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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