Variant report

Variant	rs13219456
Chromosome Location	chr6:53645566-53645567
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10456164	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10456166	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs10456167	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs10456671	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12193312	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12197259	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12211680	0.89[CHB][hapmap]
rs12213392	0.89[CHB][hapmap]
rs13191282	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13195168	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13196802	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206978	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211007	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3000995	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3003502	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4302662	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4409173	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4416674	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4428502	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4443499	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4469293	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4479931	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4555913	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4574642	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4715423	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.93[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]
rs6458955	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6909833	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6930030	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6930035	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7745277	1.00[CEU][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7755196	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7755522	0.85[EUR][1000 genomes]
rs7773640	0.85[CEU][hapmap];0.83[MEX][hapmap]

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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13219456	C6orf142	cis	cerebellum	SCAN
rs13219456	PRIM2	cis	parietal	SCAN
rs13219456	HMGCLL1	cis	parietal	SCAN
rs13219456	LRRC1	Cis_1M	lymphoblastoid	RTeQTL
rs13219456	KLHL31	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53636400-53652800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:53637600-53656000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:53639400-53658000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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