Variant report

Variant	rs2178452
Chromosome Location	chr3:160370160-160370161
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	chr3:160361430..160364332-chr3:160369380..160371394,3	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10936207	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936208	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10936209	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936210	0.87[ASN][1000 genomes]
rs11709300	0.84[EUR][1000 genomes]
rs11927913	0.87[ASN][1000 genomes]
rs12639488	0.80[CEU][hapmap]
rs13065289	0.82[EUR][1000 genomes]
rs13095931	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1317085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403045	0.83[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1522285	0.87[ASN][1000 genomes]
rs16831337	0.84[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs17236586	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879797	0.83[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.86[ASN][1000 genomes]
rs1980277	0.87[ASN][1000 genomes]
rs28544045	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28730907	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34362576	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34949451	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35308461	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35480231	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35664264	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35867836	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36118017	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3946273	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4133253	0.84[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs4679659	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4679660	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4679909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679910	0.85[EUR][1000 genomes]
rs62272215	0.84[EUR][1000 genomes]
rs62272216	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272217	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272218	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272219	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62272220	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6773389	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6773962	0.84[EUR][1000 genomes]
rs6774379	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774566	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776873	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6777739	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779581	0.96[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6779671	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6787452	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797760	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6798462	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6801373	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6803670	0.87[ASN][1000 genomes]
rs6806755	0.84[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7610939	0.84[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs7632884	0.84[EUR][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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv877703	chr3:160325458-160398885	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	esv2757019	chr3:160351021-160380161	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv2759194	chr3:160351021-160380161	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2178452	IFT80	cis	parietal	SCAN
rs2178452	KLRB1	trans	parietal	SCAN
rs2178452	SMC4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160367800-160372200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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