Variant report

Variant	rs12634879
Chromosome Location	chr3:139885338-139885339
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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];0.89[JPT][hapmap]
rs1316385	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1317898	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs1320256	0.88[CEU][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1320259	0.90[EUR][1000 genomes]
rs1320260	1.00[CEU][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs1320261	0.82[CEU][hapmap];0.90[JPT][hapmap]
rs2350275	0.90[EUR][1000 genomes]
rs2350276	0.84[EUR][1000 genomes]
rs2350281	0.88[CEU][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs2350508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2350509	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2882369	1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs2882370	0.88[CEU][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs4317058	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4596106	0.85[EUR][1000 genomes]
rs4683480	0.88[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs4683481	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs4683808	1.00[CEU][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs6439899	0.87[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6791658	0.88[CEU][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs6796645	0.84[EUR][1000 genomes]
rs7355921	0.93[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7645343	0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9283594	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289599	0.84[EUR][1000 genomes]
rs939189	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs939190	1.00[CEU][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs9817495	0.88[CEU][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9818360	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818488	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][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]
rs9822943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835717	1.00[CEU][hapmap]
rs9855981	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862740	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9862768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868890	1.00[CEU][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9871857	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9873081	0.88[EUR][1000 genomes]
rs9873941	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9878323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9990262	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]

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
rs12634879	XRN1	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139867400-139890000	Weak transcription	HSMMtube	muscle
2	chr3:139877000-139901200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:139880200-139886400	Weak transcription	NHDF-Ad	bronchial
4	chr3:139883600-139885600	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr3:139883600-139889600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:139884200-139886600	Enhancers	Ovary	ovary
7	chr3:139884400-139885400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:139884600-139886200	Weak transcription	Osteobl	bone
9	chr3:139884600-139886400	Weak transcription	NH-A	brain
10	chr3:139885000-139886200	Enhancers	Brain Cingulate Gyrus	brain
11	chr3:139885000-139886400	Enhancers	Colon Smooth Muscle	Colon
12	chr3:139885000-139887600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:139885200-139885600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:139885200-139886400	Enhancers	Brain Substantia Nigra	brain
15	chr3:139885200-139887200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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