Variant report

Variant	rs2465403
Chromosome Location	chr8:120090827-120090828
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1158945	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11994775	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13259300	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1351952	0.81[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1364708	0.88[CEU][hapmap]
rs1385491	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1385493	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.99[ASN][1000 genomes]
rs1485290	0.85[CEU][hapmap]
rs1485291	0.85[CEU][hapmap]
rs1485292	0.92[CEU][hapmap];0.95[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs1485293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs1485294	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1485299	0.85[CEU][hapmap]
rs1549415	0.88[CEU][hapmap]
rs1905774	0.92[CEU][hapmap]
rs1905775	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242313	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs2450060	0.88[CEU][hapmap]
rs2450063	0.92[CEU][hapmap]
rs2450064	0.96[CEU][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2450065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2450067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2450068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2450069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2450071	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2450072	0.82[JPT][hapmap]
rs2450073	0.88[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2450074	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2450076	0.82[JPT][hapmap]
rs2450077	0.88[CEU][hapmap]
rs2450079	0.92[CEU][hapmap]
rs2450080	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs2465370	0.88[CEU][hapmap]
rs2465385	0.81[JPT][hapmap]
rs2465390	0.86[JPT][hapmap]
rs2465392	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2465404	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2468171	0.91[CEU][hapmap]
rs4279627	0.88[CEU][hapmap]
rs7386676	0.85[CEU][hapmap]
rs7813952	0.82[JPT][hapmap]

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	nsv868916	chr8:119911943-120762250	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758169	chr8:119943309-120275750	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2759639	chr8:119943309-120275750	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2465403	NOV	cis	cerebellum	SCAN
rs2465403	TAF2	cis	cerebellum	SCAN
rs2465403	TNFRSF11B	cis	lymphoblastoid	seeQTL
rs2465403	MAL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120084600-120095200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr8:120090800-120092600	Enhancers	Cortex derived primary cultured neurospheres	brain

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