Variant report

Variant	rs9885789
Chromosome Location	chr6:54129147-54129148
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10447407	0.89[EUR][1000 genomes]
rs10456680	1.00[EUR][1000 genomes]
rs10484644	1.00[EUR][1000 genomes]
rs10948805	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10948810	0.93[CEU][hapmap]
rs12190132	1.00[EUR][1000 genomes]
rs12194521	1.00[EUR][1000 genomes]
rs12197347	1.00[EUR][1000 genomes]
rs12198031	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12198070	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12201826	1.00[EUR][1000 genomes]
rs12206200	0.89[EUR][1000 genomes]
rs12212689	0.89[EUR][1000 genomes]
rs12212836	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs1298143	0.84[CEU][hapmap]
rs16885122	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1934790	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2297980	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs3957360	0.83[CHD][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap]
rs60334573	0.89[EUR][1000 genomes]
rs62396365	0.88[EUR][1000 genomes]
rs6913087	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6913138	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6937514	0.85[CEU][hapmap]
rs73440541	0.96[EUR][1000 genomes]
rs7741347	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7746489	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7755107	1.00[EUR][1000 genomes]
rs7765626	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7773258	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7774316	0.88[EUR][1000 genomes]
rs9296744	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296745	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9296747	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9349700	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs9357793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367556	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9370276	0.85[CEU][hapmap]
rs9382311	0.85[CEU][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.90[MEX][hapmap]
rs9382318	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9382319	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9395920	0.85[CEU][hapmap]
rs9395924	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9464048	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9474779	0.89[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1020961	chr6:54101801-54133709	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1020329	chr6:54103966-54129147	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9885789	GSTA3	cis	parietal	SCAN
rs9885789	TINAG	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54121400-54131200	Weak transcription	Left Ventricle	heart
2	chr6:54121400-54131400	Weak transcription	Psoas Muscle	Psoas
3	chr6:54121800-54131400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr6:54122600-54129800	Weak transcription	Fetal Heart	heart
5	chr6:54124800-54129200	Enhancers	Fetal Intestine Large	intestine
6	chr6:54126000-54129200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:54128600-54129800	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr6:54128800-54131400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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