Variant report

Variant	rs950719
Chromosome Location	chr6:12774214-12774215
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1011188	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10434855	0.91[EUR][1000 genomes]
rs10498681	0.80[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12525116	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12525210	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12526812	0.80[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12528247	0.96[EUR][1000 genomes]
rs12528721	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1332842	0.80[EUR][1000 genomes]
rs1332851	0.90[MEX][hapmap]
rs1571996	0.80[CEU][hapmap];0.91[EUR][1000 genomes]
rs1572001	0.80[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17616767	0.89[CEU][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17617491	0.91[EUR][1000 genomes]
rs17617584	1.00[TSI][hapmap]
rs17678734	0.80[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17679286	0.91[EUR][1000 genomes]
rs2015761	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2151221	0.80[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2876298	0.80[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];1.00[EUR][1000 genomes]
rs35278288	0.80[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs4285318	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4293998	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4577783	1.00[ASW][hapmap];0.80[CEU][hapmap];0.83[GIH][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]
rs4583985	0.80[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4711817	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4711856	0.80[MEX][hapmap];0.80[EUR][1000 genomes]
rs4714931	0.91[EUR][1000 genomes]
rs55764622	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55879442	0.96[EUR][1000 genomes]
rs56244510	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56259669	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56270763	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58666803	0.87[EUR][1000 genomes]
rs60954427	0.87[EUR][1000 genomes]
rs6915585	0.80[CEU][hapmap];0.91[EUR][1000 genomes]
rs73722820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73722822	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73722823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73722845	0.96[EUR][1000 genomes]
rs73722849	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7768030	0.80[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs9369607	0.91[EUR][1000 genomes]
rs9369612	0.80[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs9381451	0.80[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs9463091	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9463093	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9463105	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9463114	0.80[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9463117	0.80[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9463119	0.80[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9463140	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9472484	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9472511	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9472512	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9472513	0.80[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9472514	0.80[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9472519	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9472520	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9472528	0.80[CEU][hapmap];0.91[MEX][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9472549	0.80[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9472566	0.80[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9473093	1.00[CHD][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	esv3521000	chr6:12561306-13128519	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3521001	chr6:12561306-13128519	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv830587	chr6:12769661-12939875	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs950719	NEDD9	cis	cerebellum	SCAN
rs950719	MAP3K5	trans	lymphoblastoid	seeQTL
rs950719	RORA	trans	lymphoblastoid	seeQTL
rs950719	PHACTR1	cis	cerebellum	SCAN
rs950719	IL18R1	trans	lymphoblastoid	seeQTL
rs950719	IL1R2	trans	lymphoblastoid	seeQTL
rs950719	MYLIP	cis	parietal	SCAN
rs950719	PHF16	trans	lymphoblastoid	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12762200-12780600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr6:12770600-12775000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:12770600-12775800	Weak transcription	HSMMtube	muscle
4	chr6:12770800-12776200	Weak transcription	HSMM	muscle
5	chr6:12773800-12780400	Weak transcription	Fetal Brain Female	brain
6	chr6:12774000-12780400	Weak transcription	Fetal Brain Male	brain

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