Variant report

Variant	rs553989
Chromosome Location	chr3:47400328-47400329
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1038394	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10865946	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11130127	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11705957	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11711824	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11712445	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11719877	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11925823	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11927371	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12486969	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12487736	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12497225	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12632132	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12636851	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13064843	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13075233	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13079098	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1531875	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17410853	0.80[EUR][1000 genomes]
rs17411375	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1872164	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2062278	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2159400	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295428	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295449	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295458	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295461	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3736177	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4241548	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4858805	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4858848	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4858868	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4858888	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858890	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4858894	0.80[AMR][1000 genomes]
rs56032309	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56351005	0.86[EUR][1000 genomes]
rs57346147	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60369822	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62246474	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62248580	0.80[EUR][1000 genomes]
rs6787422	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6792461	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6800271	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7613282	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7641010	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7649234	0.83[AMR][1000 genomes]
rs7651762	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs807810	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs807931	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8180040	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs922957	0.83[AMR][1000 genomes];0.88[EUR][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	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	esv1807553	chr3:47393616-47470763	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv3802	chr3:47396674-47441951	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs553989	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs553989	SETD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47386800-47400800	Weak transcription	Pancreas	Pancrea
2	chr3:47388000-47400600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:47398600-47401800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood

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