Variant report

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10986631	0.93[ASN][1000 genomes]
rs10986638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10986647	0.87[ASN][1000 genomes]
rs16916777	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs16916909	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17778184	0.91[CEU][hapmap]
rs1930409	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1999502	0.93[ASN][1000 genomes]
rs1999503	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2001992	0.93[ASN][1000 genomes]
rs2779558	1.00[JPT][hapmap]
rs2779569	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2779576	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2808568	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4237192	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4507885	0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs4743234	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4743237	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62576023	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62576024	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7045028	0.82[YRI][hapmap]
rs7857537	0.82[YRI][hapmap]
rs871002	0.87[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap]
rs884886	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs9408972	1.00[JPT][hapmap]
rs944760	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs944762	0.85[CHB][hapmap];1.00[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	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv831665	chr9:101170061-101367692	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv6633	chr9:101308371-101342811	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2900512	C9orf3	cis	cerebellum	SCAN
rs2900512	LPPR1	cis	cerebellum	SCAN
rs2900512	RNF20	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101314400-101326400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:101314600-101320800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr9:101315200-101320400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:101315400-101318400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr9:101315600-101318000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr9:101317800-101318800	Enhancers	Cortex derived primary cultured neurospheres	brain

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