Variant report

Variant	rs205946
Chromosome Location	chr6:118494825-118494826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11964013	1.00[CHD][hapmap];0.82[JPT][hapmap]
rs11967448	0.82[JPT][hapmap]
rs1334829	0.82[JPT][hapmap]
rs1334835	0.82[JPT][hapmap]
rs169542	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs172239	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176168	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2011710	1.00[CHD][hapmap]
rs205926	0.85[JPT][hapmap]
rs205928	0.85[JPT][hapmap]
rs205931	0.85[JPT][hapmap]
rs205935	0.85[JPT][hapmap]
rs205936	1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs205937	1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs205938	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs205939	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs205940	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs205941	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs205943	1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs205944	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs205945	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs205947	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs205948	1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs205949	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs205952	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs205960	0.82[JPT][hapmap]
rs205964	0.82[JPT][hapmap]
rs205969	0.82[JPT][hapmap]
rs205970	0.82[JPT][hapmap]
rs205973	0.82[JPT][hapmap]
rs2105019	1.00[CHD][hapmap];0.82[JPT][hapmap]
rs2484144	0.82[JPT][hapmap]
rs2484145	0.82[JPT][hapmap]
rs2484149	0.82[JPT][hapmap]
rs2501519	1.00[CHD][hapmap];0.82[JPT][hapmap]
rs2859147	0.82[JPT][hapmap]
rs73523952	1.00[ASN][1000 genomes]
rs928597	0.82[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	nsv530526	chr6:118027339-118718476	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv428153	chr6:118430517-118586974	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1030089	chr6:118436482-118604516	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv538427	chr6:118436482-118604516	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs205946	FCER2	trans	brain	seeQTL
rs205946	GPR3	trans	brain	seeQTL
rs205946	LAMB3	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118494200-118495000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:118494600-118495200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:118494600-118496200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:118494600-118496200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain

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