Variant report

Variant	rs17678734
Chromosome Location	chr6:12770843-12770844
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1011188	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10434855	0.91[EUR][1000 genomes]
rs10498681	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12525116	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12525210	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12526812	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12528247	0.96[EUR][1000 genomes]
rs12528721	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12530470	0.89[CEU][hapmap]
rs1332842	0.80[EUR][1000 genomes]
rs1332851	0.89[CEU][hapmap];0.90[MEX][hapmap]
rs1571996	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1572001	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16873301	0.81[CEU][hapmap]
rs17616767	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17617491	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17617584	1.00[TSI][hapmap]
rs17679286	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2015761	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2151221	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2876298	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];1.00[EUR][1000 genomes]
rs35278288	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs4285318	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4293998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4577783	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4583985	1.00[CEU][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4711817	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4711856	0.80[MEX][hapmap];0.80[EUR][1000 genomes]
rs4714931	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs55764622	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55879442	0.96[EUR][1000 genomes]
rs56244510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56259669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56270763	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58666803	0.87[EUR][1000 genomes]
rs60954427	0.87[EUR][1000 genomes]
rs6911996	0.89[CEU][hapmap]
rs6915585	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs73722820	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73722822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73722823	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73722845	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs73722849	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7768030	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs9357486	0.89[CEU][hapmap]
rs9369607	0.91[EUR][1000 genomes]
rs9369612	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs9381451	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs9463091	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9463093	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9463105	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9463114	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9463117	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9463119	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9463140	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9472484	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9472511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9472512	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9472513	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9472514	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9472519	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9472520	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9472528	1.00[CEU][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9472549	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9472566	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs950719	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]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17678734	PHACTR1	cis	cerebellum	SCAN
rs17678734	MYLIP	cis	parietal	SCAN
rs17678734	IL1R2	trans	lymphoblastoid	seeQTL
rs17678734	NEDD9	cis	cerebellum	SCAN

Chromatin state (count:7 , 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	chr6:12769400-12773800	Enhancers	Fetal Brain Female	brain
3	chr6:12769600-12774000	Enhancers	Fetal Brain Male	brain
4	chr6:12770600-12775000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:12770600-12775800	Weak transcription	HSMMtube	muscle
6	chr6:12770800-12771000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:12770800-12776200	Weak transcription	HSMM	muscle

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