Variant report

Variant	rs6481485
Chromosome Location	chr10:28123364-28123365
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10763626	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11006736	1.00[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs11595836	0.80[AFR][1000 genomes]
rs12355412	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12355413	1.00[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs12771348	0.83[CEU][hapmap]
rs12771925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547327	0.91[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1812592	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1889522	0.92[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2152019	0.84[CHD][hapmap];0.87[GIH][hapmap]
rs2368266	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4749273	0.80[GIH][hapmap]
rs6481484	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6481486	0.84[AFR][1000 genomes]
rs7078534	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085331	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7085555	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7093199	0.82[AFR][1000 genomes]
rs7475103	0.83[AFR][1000 genomes]
rs7898085	0.83[AFR][1000 genomes]
rs7908626	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs915174	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs915175	0.86[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[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	nsv831813	chr10:28017606-28200651	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv971859	chr10:28070066-28271252	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6481485	KIAA1217	cis	parietal	SCAN
rs6481485	ZNF79	trans	cerebellum	SCAN
rs6481485	HIST2H2BE	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28105600-28127600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr10:28121000-28158600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:28122800-28123400	Active TSS	Spleen	Spleen
4	chr10:28123200-28123600	Enhancers	Ovary	ovary

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