Variant report

Variant	rs687339
Chromosome Location	chr3:135932359-135932360
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	chr3:135915739..135918112-chr3:135931092..135933753,3	K562	blood:
2	chr3:135928475..135930111-chr3:135931628..135934340,2	K562	blood:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10935177	1.00[JPT][hapmap]
rs1145101	0.83[MEX][hapmap]
rs1145106	0.81[JPT][hapmap];0.88[MEX][hapmap]
rs1153870	0.83[ASN][1000 genomes]
rs1153871	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1153872	0.84[ASN][1000 genomes]
rs1153877	0.86[JPT][hapmap]
rs1154988	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12330635	0.88[CHB][hapmap]
rs1278493	1.00[JPT][hapmap]
rs1278719	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1279086	0.86[JPT][hapmap]
rs1279425	0.84[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap]
rs1279831	1.00[JPT][hapmap]
rs1279840	0.84[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.80[TSI][hapmap]
rs1711171	0.84[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap]
rs17252498	0.83[CEU][hapmap]
rs2655008	0.81[JPT][hapmap]
rs3755636	0.88[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3772390	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs3821445	0.88[CEU][hapmap];0.83[MEX][hapmap]
rs3957816	1.00[JPT][hapmap]
rs4678322	0.80[EUR][1000 genomes]
rs4678361	0.82[EUR][1000 genomes]
rs4678428	0.84[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap]
rs483465	0.84[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap]
rs518972	0.86[JPT][hapmap]
rs523118	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs534944	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs548288	0.84[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.80[TSI][hapmap];0.81[ASN][1000 genomes]
rs556788	0.86[JPT][hapmap]
rs571513	0.86[JPT][hapmap];0.83[MEX][hapmap]
rs576771	0.84[CEU][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap]
rs589092	0.86[JPT][hapmap]
rs606725	0.84[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap]
rs610860	0.88[CEU][hapmap]
rs61789561	0.82[EUR][1000 genomes]
rs61791721	0.83[EUR][1000 genomes]
rs61791757	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs619605	0.81[JPT][hapmap]
rs645040	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs650326	0.86[JPT][hapmap]
rs654237	0.81[JPT][hapmap]
rs655836	0.81[JPT][hapmap]
rs661739	1.00[JPT][hapmap]
rs667920	0.86[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap]
rs6779146	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs684773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs695983	0.81[JPT][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap]
rs696081	0.86[JPT][hapmap]
rs696516	0.81[JPT][hapmap];0.83[MEX][hapmap]
rs696517	0.88[CEU][hapmap];0.88[MEX][hapmap]
rs696518	0.81[JPT][hapmap]
rs696520	0.86[JPT][hapmap]
rs698270	0.81[JPT][hapmap];0.88[MEX][hapmap]
rs7372313	1.00[JPT][hapmap]
rs895893	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs895894	1.00[JPT][hapmap]
rs9810089	0.86[JPT][hapmap]
rs9811753	0.85[JPT][hapmap]
rs9840812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs9845457	1.00[JPT][hapmap]
rs9848883	0.88[CHB][hapmap]
rs9856769	0.88[CHB][hapmap]
rs9865841	0.82[EUR][1000 genomes]

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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv508246	chr3:135922023-136038622	Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs687339	PCCB	cis	lymphoblastoid	seeQTL
rs687339	NCK1	cis	parietal	SCAN
rs687339	MSL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135930800-135934200	Enhancers	Liver	Liver
2	chr3:135931400-135933400	Enhancers	HepG2	liver

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