Variant report

Variant	rs9485530
Chromosome Location	chr6:102119829-102119830
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10485273	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10872738	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap]
rs10872739	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1222958	0.95[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1222960	0.86[ASN][1000 genomes]
rs1337412	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1337415	0.93[CHD][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1337424	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1415485	0.83[CHB][hapmap]
rs1415489	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1832293	0.86[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1856133	0.81[CEU][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2065938	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs2105118	0.86[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2225865	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2518294	0.84[AMR][1000 genomes]
rs2518295	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2518303	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2786251	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs2786254	0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2852560	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2852565	0.86[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap]
rs4839800	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs6904687	1.00[CHB][hapmap]
rs6907727	0.81[GIH][hapmap]
rs6923409	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap]
rs7451268	0.80[YRI][hapmap]
rs9322602	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9322603	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9390768	0.83[CHB][hapmap]
rs9485526	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9485532	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9498658	0.91[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9498659	0.90[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9498662	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9498663	0.91[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9498664	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9498667	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv538392	chr6:101938381-102148360	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv3384771	chr6:101996253-102283808	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1032499	chr6:102069885-102720998	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv463993	chr6:102084491-102165329	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv604317	chr6:102084491-102165329	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv527973	chr6:102114780-102119829	Enhancers Weak transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9485530	PRDM13	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:102114600-102121600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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