Variant report

Variant	rs2250857
Chromosome Location	chr1:86873094-86873095
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10493789	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs10747328	0.85[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs10873777	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs11161820	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1158505	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs12564227	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1334143	0.80[CHB][hapmap];0.85[ASN][1000 genomes]
rs1334146	0.82[ASN][1000 genomes]
rs1334147	0.85[ASN][1000 genomes]
rs1334148	0.83[ASN][1000 genomes]
rs1334150	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17129055	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17129078	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs185655	0.80[CHB][hapmap]
rs187971	0.81[ASN][1000 genomes]
rs1931363	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs2104963	0.86[ASN][1000 genomes]
rs2151708	0.86[ASN][1000 genomes]
rs2151709	0.85[ASN][1000 genomes]
rs2249296	0.92[ASW][hapmap];0.86[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2252313	0.85[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs272491	0.85[CHB][hapmap]
rs272498	0.93[CHB][hapmap]
rs272504	0.85[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs272507	0.85[CHB][hapmap]
rs2791464	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3765975	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs3765978	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4288573	0.80[ASN][1000 genomes]
rs4292929	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61800656	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61804060	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6695671	0.85[CHB][hapmap]
rs883200	0.86[ASN][1000 genomes]
rs9433030	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9787365	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]

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	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871081	chr1:86806372-86892819	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2250857	LOC339524	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86862400-86876400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:86872800-86875200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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