Variant report

Variant	rs2518319
Chromosome Location	chr6:101799259-101799260
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:101798733..101801184-chr6:101804475..101806686,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1160258	0.83[ASN][1000 genomes]
rs1338156	0.92[AFR][1000 genomes]
rs1415946	0.80[MEX][hapmap];0.86[YRI][hapmap]
rs17658674	0.83[ASN][1000 genomes]
rs1948050	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2518173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2518174	0.97[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2518177	0.92[AFR][1000 genomes]
rs2518320	0.97[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2579928	0.88[AFR][1000 genomes]
rs2579929	0.82[EUR][1000 genomes]
rs2579930	0.90[AFR][1000 genomes]
rs2629982	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2629983	0.85[AFR][1000 genomes]
rs2787573	0.82[EUR][1000 genomes]
rs283186	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs283227	0.83[AFR][1000 genomes]
rs283229	0.83[AFR][1000 genomes]
rs2852497	0.88[EUR][1000 genomes]
rs2852500	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852502	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852503	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852504	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852505	0.82[EUR][1000 genomes]
rs2852506	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852507	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852508	0.80[MEX][hapmap];0.86[YRI][hapmap]
rs2852509	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852510	0.82[EUR][1000 genomes]
rs2852511	1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852512	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852513	0.82[EUR][1000 genomes]
rs2852514	0.82[EUR][1000 genomes]
rs471631	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473846	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480221	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484819	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489458	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493123	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500305	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503387	0.88[EUR][1000 genomes]
rs504406	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504408	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs528879	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542820	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542923	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546327	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566507	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570556	0.81[EUR][1000 genomes]
rs577503	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579069	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs584655	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs594870	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600842	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608847	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs632956	0.81[EUR][1000 genomes]
rs636796	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638255	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs661064	0.88[EUR][1000 genomes]
rs662360	0.84[EUR][1000 genomes]
rs662916	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs668267	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675259	0.85[EUR][1000 genomes]
rs683149	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684160	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs685002	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs687497	0.85[EUR][1000 genomes]
rs697440	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs697441	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808952	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2518319	TOX3	trans	lymphoblastoid	seeQTL
rs2518319	SNX7	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101799000-101799600	Enhancers	NHEK	skin
2	chr6:101799200-101800000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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