Variant report

Variant	rs888466
Chromosome Location	chr12:4533605-4533606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1019398	0.95[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10849063	0.84[ASN][1000 genomes]
rs10849064	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10849069	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11063150	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11608707	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11610220	0.81[CEU][hapmap]
rs11610225	0.81[CEU][hapmap]
rs11610929	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612742	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615557	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12367170	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368351	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241283	0.95[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2244388	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2970805	0.86[EUR][1000 genomes]
rs2970806	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4766242	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766243	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766244	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766246	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4766247	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4766248	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61909562	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7131828	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295812	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299949	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7304520	0.84[ASN][1000 genomes]
rs7316012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv557123	chr12:4436632-4736569	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv898616	chr12:4490059-4564613	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv585	chr12:4514249-4559242	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs888466	FOXJ2	cis	parietal	SCAN
rs888466	FBXL14	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4533200-4534000	Enhancers	Fetal Muscle Leg	muscle
2	chr12:4533200-4542200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr12:4533400-4549000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:4533600-4534000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr12:4533600-4534000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:4533600-4534000	Enhancers	Fetal Lung	lung

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