Variant report

Variant	rs12950390
Chromosome Location	chr17:45830948-45830949
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45828857..45831550-chr17:45834956..45836482,2	K562	blood:
2	chr17:45771741..45773536-chr17:45828726..45831612,2	K562	blood:

Variant related genes	Relation type
ENSG00000198933	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10445375	0.86[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs10445376	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11079786	0.82[JPT][hapmap]
rs11079789	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11079790	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11079791	0.86[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.92[ASN][1000 genomes]
rs11079792	0.86[ASN][1000 genomes]
rs11651842	0.86[ASN][1000 genomes]
rs11655336	0.86[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.92[ASN][1000 genomes]
rs12325760	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12450729	0.94[ASN][1000 genomes]
rs12450733	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12451815	0.86[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12453955	0.86[ASN][1000 genomes]
rs12721470	0.88[CHD][hapmap]
rs17244587	0.88[CHD][hapmap]
rs17700008	0.86[ASN][1000 genomes]
rs17773010	0.92[ASN][1000 genomes]
rs2074190	0.82[JPT][hapmap]
rs28589850	0.94[ASN][1000 genomes]
rs4239165	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4239166	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4793646	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4793647	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4794063	0.82[JPT][hapmap]
rs4794067	0.82[JPT][hapmap]
rs4794110	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55745341	0.94[ASN][1000 genomes]
rs56137679	0.81[ASN][1000 genomes]
rs56363619	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56387656	0.92[ASN][1000 genomes]
rs58391889	0.86[ASN][1000 genomes]
rs59513807	0.86[ASN][1000 genomes]
rs6503855	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66471233	0.86[ASN][1000 genomes]
rs67441169	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72831644	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8068453	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8071192	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs8078052	0.92[ASN][1000 genomes]

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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv2071	chr17:45801503-45844229	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	esv1811624	chr17:45825220-45846505	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
IgG glycosylation	23382691	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12950390	TBKBP1	cis	cerebellum	SCAN
rs12950390	ETNK2	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45824400-45831800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:45830000-45831200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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