Variant report

Variant	rs9990262
Chromosome Location	chr3:139872048-139872049
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139868037..139869818-chr3:139871786..139873761,2	K562	blood:
2	chr3:139864319..139866124-chr3:139869946..139872757,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12494072	0.87[ASW][hapmap];0.82[CEU][hapmap]
rs12634879	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1316385	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1317898	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1320256	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs1320259	0.89[EUR][1000 genomes]
rs1320260	1.00[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs1320261	0.82[CEU][hapmap]
rs2350275	0.89[EUR][1000 genomes]
rs2350276	0.83[EUR][1000 genomes]
rs2350281	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs2350508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2350509	0.89[EUR][1000 genomes]
rs2882369	1.00[CEU][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs2882370	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs4317058	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4596106	0.84[EUR][1000 genomes]
rs4683480	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs4683481	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4683808	1.00[CEU][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs6439899	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs6791658	0.88[CEU][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs6796645	0.83[EUR][1000 genomes]
rs7355921	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs7645343	0.91[EUR][1000 genomes]
rs9283594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9289599	0.83[EUR][1000 genomes]
rs939189	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs939190	1.00[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs9817495	0.88[CEU][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs9818360	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs9818488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9822943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9823483	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9835717	1.00[CEU][hapmap]
rs9855981	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9862740	0.95[EUR][1000 genomes]
rs9862768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9868890	1.00[CEU][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9871857	0.90[EUR][1000 genomes]
rs9873081	0.88[EUR][1000 genomes]
rs9873941	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9878323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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	nsv998423	chr3:139526446-139947336	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv829739	chr3:139797496-140002685	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9990262	XRN1	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139866000-139874400	Weak transcription	Ovary	ovary
2	chr3:139867400-139890000	Weak transcription	HSMMtube	muscle
3	chr3:139870400-139872800	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr3:139871400-139872400	Enhancers	Psoas Muscle	Psoas
5	chr3:139871400-139872800	Enhancers	Fetal Heart	heart
6	chr3:139871400-139872800	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr3:139871600-139872600	Enhancers	Brain Germinal Matrix	brain
8	chr3:139871800-139872200	Enhancers	Left Ventricle	heart
9	chr3:139871800-139872600	Enhancers	Fetal Muscle Leg	muscle
10	chr3:139871800-139872800	Enhancers	Right Ventricle	heart

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