Variant report

Variant	rs182411
Chromosome Location	chr1:76049897-76049898
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1332784	0.91[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap]
rs1332790	0.84[ASN][1000 genomes]
rs17303921	0.91[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap]
rs211675	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs211678	0.85[ASN][1000 genomes]
rs211679	0.85[ASN][1000 genomes]
rs211683	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap]
rs211696	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs211759	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap]
rs211762	0.81[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs211786	0.85[CHB][hapmap]
rs377233	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs396106	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs398851	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs409544	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs417258	0.83[ASN][1000 genomes]
rs434424	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs438611	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs645742	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][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	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv3445096	chr1:75933216-76126980	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv2757737	chr1:75986904-76187748	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv2758943	chr1:75986904-76187748	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs182411	SLC44A5	cis	cerebellum	SCAN
rs182411	IFI44	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76049600-76054600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:76049800-76053600	Weak transcription	Fetal Brain Male	brain
3	chr1:76049800-76054600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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