Variant report

Variant	rs12498317
Chromosome Location	chr4:56007093-56007094
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:55991727..55995613-chr4:56004495..56007704,3	K562	blood:

Variant related genes	Relation type
ENSG00000128052	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10012589	0.99[ASN][1000 genomes]
rs10012701	0.99[ASN][1000 genomes]
rs10013070	0.92[AFR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10013228	0.98[ASN][1000 genomes]
rs10020668	0.98[ASN][1000 genomes]
rs10026340	0.92[AFR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10517343	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.99[ASN][1000 genomes]
rs12331471	0.99[ASN][1000 genomes]
rs12331507	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12331538	0.98[ASN][1000 genomes]
rs12331597	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12505096	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1350545	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1380068	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1551641	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1551642	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1551643	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1551644	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1551645	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17711225	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17711320	0.98[ASN][1000 genomes]
rs17773813	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1903068	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239702	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.96[ASN][1000 genomes]
rs28411232	0.98[ASN][1000 genomes]
rs28517654	0.98[ASN][1000 genomes]
rs28584303	0.94[ASN][1000 genomes]
rs28680424	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28838369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36146043	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36190491	0.95[ASN][1000 genomes]
rs41408948	0.96[ASN][1000 genomes]
rs4516787	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73236104	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs73236106	0.98[ASN][1000 genomes]
rs73236109	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73236111	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9284955	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9312655	1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[YRI][hapmap];0.99[ASN][1000 genomes]
rs9312656	0.99[ASN][1000 genomes]
rs9312657	0.99[ASN][1000 genomes]
rs9312658	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9992737	0.98[ASN][1000 genomes]
rs9997685	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9998950	0.92[AFR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12498317	SPATA18	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55999600-56020600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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