Variant report

Variant	rs1490388
Chromosome Location	chr6:126835655-126835656
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10457478	1.00[ASN][1000 genomes]
rs1155939	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1159619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202204	1.00[ASN][1000 genomes]
rs1361108	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1361262	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1490384	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1490387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1538172	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1538956	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1578060	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1591805	1.00[ASN][1000 genomes]
rs1602278	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17754780	0.90[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1826189	0.93[AFR][1000 genomes]
rs1907067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2027299	0.85[EUR][1000 genomes]
rs2039735	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2045258	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2050644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2130603	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2326387	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34539692	1.00[ASN][1000 genomes]
rs3861455	0.96[AFR][1000 genomes]
rs3905044	0.85[AFR][1000 genomes]
rs4053271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243491	0.90[AFR][1000 genomes]
rs4422634	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4626447	0.87[AFR][1000 genomes]
rs4895807	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895808	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895813	0.85[AFR][1000 genomes]
rs59698523	0.80[EUR][1000 genomes]
rs6907898	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911485	0.82[AFR][1000 genomes]
rs6919397	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921183	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6925689	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7738135	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743860	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap]
rs853961	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs9321065	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375435	0.90[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375442	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9375446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375447	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9388486	0.90[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388487	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388489	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388490	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388500	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9388507	0.85[AFR][1000 genomes]
rs9398803	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398804	0.86[EUR][1000 genomes]
rs9401876	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9401885	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9401888	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9491624	1.00[CHB][hapmap];0.87[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	nsv1021636	chr6:126792916-127022489	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1026498	chr6:126812609-127397240	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Height	18391951	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1490388	C6orf174	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:126825800-126844800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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