Variant report

Variant	rs9376452
Chromosome Location	chr6:140016409-140016410
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:140016247..140019706-chr6:140025179..140028113,3	K562	blood:
2	chr6:139693240..139695789-chr6:140014920..140018610,3	K562	blood:
3	chr6:139694131..139695789-chr6:140016107..140019302,3	K562	blood:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10499213	0.88[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs11962730	0.80[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs11963532	0.86[AFR][1000 genomes]
rs11964275	0.88[JPT][hapmap]
rs12055436	0.93[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12055472	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12055843	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12662206	0.88[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs12664473	0.81[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs17069206	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17069225	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1891808	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1936210	0.88[ASN][1000 genomes]
rs2096283	0.88[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs2096284	0.87[ASW][hapmap];0.80[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2154032	0.80[GIH][hapmap];0.88[JPT][hapmap]
rs2185923	0.90[ASN][1000 genomes]
rs2327993	0.90[ASN][1000 genomes]
rs55764205	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60350063	0.89[AFR][1000 genomes]
rs60758082	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60870127	0.99[ASN][1000 genomes]
rs6570372	0.88[ASN][1000 genomes]
rs6570373	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6570374	0.88[JPT][hapmap]
rs6901783	0.81[JPT][hapmap]
rs6905478	0.80[GIH][hapmap];0.82[JPT][hapmap]
rs6933318	0.81[JPT][hapmap]
rs73556090	0.90[ASN][1000 genomes]
rs73558032	0.90[AFR][1000 genomes]
rs7752001	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7752323	0.88[ASN][1000 genomes]
rs7774968	0.88[JPT][hapmap]
rs9321752	0.90[ASN][1000 genomes]
rs9373246	0.80[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9373247	0.88[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs9373248	0.86[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs9376457	0.88[ASN][1000 genomes]
rs9385874	0.88[JPT][hapmap]
rs9385876	0.88[JPT][hapmap]
rs9389715	0.88[ASN][1000 genomes]
rs9389717	0.88[JPT][hapmap]
rs9399292	0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9403113	0.86[ASN][1000 genomes]
rs9403115	0.88[JPT][hapmap]
rs9403116	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv516840	chr6:139960833-140053704	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9376452	IL22RA2	cis	cerebellum	SCAN
rs9376452	MAP3K5	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140012200-140016800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr6:140015600-140017000	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr6:140015800-140019800	Weak transcription	Liver	Liver
4	chr6:140016000-140017400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr6:140016200-140017200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:140016200-140017200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr6:140016400-140016600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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