Variant report

Variant	rs12055436
Chromosome Location	chr6:140023968-140023969
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	chr6:139694333..139696557-chr6:140022080..140025320,3	MCF-7	breast:
2	chr6:140017766..140019321-chr6:140022957..140024761,2	K562	blood:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10499213	0.82[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10499214	0.88[ASN][1000 genomes]
rs11962730	0.80[ASW][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];0.81[MEX][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11963532	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11964275	0.82[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs12055472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12055843	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12662206	0.82[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12664473	0.82[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs17069206	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17069225	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][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]
rs1891808	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1936210	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1936214	0.88[ASN][1000 genomes]
rs2096283	0.82[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2096284	0.93[ASW][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];0.81[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2154032	0.82[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs2185923	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2327993	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4520026	0.88[ASN][1000 genomes]
rs55764205	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55966840	0.88[ASN][1000 genomes]
rs60350063	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs60758082	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60870127	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6570372	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6570373	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6570374	0.81[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs6901783	0.81[JPT][hapmap]
rs6905478	0.82[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs6933318	0.81[JPT][hapmap]
rs73556090	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73558032	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7743796	0.88[ASN][1000 genomes]
rs7752001	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7752323	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7756866	0.88[ASN][1000 genomes]
rs7769567	0.86[ASN][1000 genomes]
rs7774968	0.82[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs9321752	0.99[ASN][1000 genomes]
rs9373246	0.87[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9373247	0.82[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9373248	0.82[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9376452	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]
rs9376457	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9385874	0.82[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs9385875	0.88[ASN][1000 genomes]
rs9385876	0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs9389715	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9389717	0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs9399292	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9403113	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9403114	0.88[ASN][1000 genomes]
rs9403115	0.82[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs9403116	0.87[JPT][hapmap];0.88[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	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
3	nsv823851	chr6:140019537-140024421	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12055436	MAP3K5	cis	parietal	SCAN
rs12055436	IL22RA2	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140022400-140029200	Weak transcription	NHDF-Ad	bronchial
2	chr6:140022600-140028000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:140023600-140024200	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr6:140023600-140024600	Enhancers	Primary monocytes fromperipheralblood	blood

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