Variant report

Variant	rs9879189
Chromosome Location	chr3:54538880-54538881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11706275	0.96[CEU][hapmap]
rs11708855	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs11713519	0.88[EUR][1000 genomes]
rs11714447	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs13082611	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap]
rs17747001	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs17747054	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs2053862	0.81[CHB][hapmap]
rs2884804	0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap]
rs6414584	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs6445673	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs6445682	0.85[CHB][hapmap]
rs6445684	0.91[CHB][hapmap]
rs6445685	0.91[CHB][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes]
rs6445687	0.80[AFR][1000 genomes]
rs6789926	0.81[CHB][hapmap]
rs6790503	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs6795380	0.91[CHB][hapmap]
rs6796049	0.96[CEU][hapmap]
rs6798952	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs7372453	0.83[EUR][1000 genomes]
rs7372541	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs7373217	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7373390	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7373932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7374204	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.86[ASN][1000 genomes]
rs7432776	0.88[CEU][hapmap];1.00[TSI][hapmap]
rs7614229	0.92[CEU][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs7636708	0.91[CHB][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap]
rs9820301	0.91[EUR][1000 genomes]
rs9855891	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap]

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	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv876810	chr3:54480798-54585416	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9879189	TEX264	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54536800-54545600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr3:54538600-54541000	Weak transcription	Spleen	Spleen

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