Variant report

Variant	rs6797299
Chromosome Location	chr3:49609794-49609795
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49603222..49606574-chr3:49608966..49612068,4	K562	blood:
2	chr3:49598309..49602377-chr3:49605664..49611011,5	K562	blood:
3	chr3:49609338..49612017-chr3:49707292..49709835,2	K562	blood:

Extended variants
information (count: 96 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10452032	0.94[CEU][hapmap];0.94[YRI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1078341	0.94[CEU][hapmap];0.94[YRI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10865956	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1106620	0.85[AFR][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11130204	0.85[AFR][1000 genomes]
rs11130207	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130208	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130211	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11130217	0.89[CEU][hapmap];0.94[YRI][hapmap];1.00[ASN][1000 genomes]
rs11709734	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11710434	1.00[ASN][1000 genomes]
rs11720542	1.00[ASN][1000 genomes]
rs11720657	1.00[ASN][1000 genomes]
rs11720705	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11721148	0.84[AMR][1000 genomes]
rs12583	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12637313	0.94[CEU][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12715437	0.94[CEU][hapmap];0.94[YRI][hapmap];1.00[ASN][1000 genomes]
rs13096480	0.93[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13322887	0.94[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1352889	0.94[CEU][hapmap];0.84[AMR][1000 genomes]
rs1463728	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491983	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1491985	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs1532204	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1586827	0.94[CEU][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1982861	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs2029591	1.00[CEU][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131108	0.94[CEU][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	0.94[YRI][hapmap];1.00[ASN][1000 genomes]
rs2177268	0.94[YRI][hapmap];1.00[ASN][1000 genomes]
rs2312462	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs2329021	0.94[CEU][hapmap];0.94[YRI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3020779	0.94[CEU][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs3448	1.00[ASN][1000 genomes]
rs34890793	1.00[CEU][hapmap]
rs4052546	0.90[AFR][1000 genomes]
rs4241405	1.00[CEU][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241407	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs4855833	0.94[CEU][hapmap];0.84[AMR][1000 genomes]
rs4855837	0.90[AFR][1000 genomes]
rs4855838	0.81[AFR][1000 genomes]
rs4855845	0.94[CEU][hapmap];0.94[YRI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4855846	0.94[CEU][hapmap];0.94[YRI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4855848	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4855849	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4855853	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4855882	0.94[CEU][hapmap]
rs4855885	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs4955430	1.00[ASN][1000 genomes]
rs56127630	1.00[ASN][1000 genomes]
rs62259933	1.00[ASN][1000 genomes]
rs62259943	1.00[ASN][1000 genomes]
rs62259944	1.00[ASN][1000 genomes]
rs62259947	1.00[ASN][1000 genomes]
rs62261249	1.00[ASN][1000 genomes]
rs62262672	1.00[ASN][1000 genomes]
rs62262673	1.00[ASN][1000 genomes]
rs62262675	1.00[ASN][1000 genomes]
rs6446275	1.00[ASN][1000 genomes]
rs6446284	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446285	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446286	1.00[ASN][1000 genomes]
rs6774202	0.94[CEU][hapmap];0.80[AMR][1000 genomes]
rs6785045	1.00[ASN][1000 genomes]
rs6805609	1.00[ASN][1000 genomes]
rs6809204	1.00[ASN][1000 genomes]
rs72934271	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73088137	1.00[ASN][1000 genomes]
rs7355800	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7613491	1.00[ASN][1000 genomes]
rs7628207	0.94[CEU][hapmap]
rs7638750	1.00[ASN][1000 genomes]
rs7644148	0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs7647973	1.00[ASN][1000 genomes]
rs7648995	1.00[ASN][1000 genomes]
rs7651372	1.00[ASN][1000 genomes]
rs8897	0.94[YRI][hapmap];1.00[ASN][1000 genomes]
rs9817807	1.00[ASN][1000 genomes]
rs9823134	0.82[YRI][hapmap]
rs9824435	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs9830730	0.94[CEU][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9835157	0.94[CEU][hapmap];0.94[YRI][hapmap]
rs9838096	0.82[YRI][hapmap]
rs9842132	1.00[ASN][1000 genomes]
rs9849038	0.94[CEU][hapmap]
rs9850501	0.82[YRI][hapmap]
rs9860055	0.94[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9860285	1.00[ASN][1000 genomes]
rs9861027	1.00[ASN][1000 genomes]
rs9870858	0.94[CEU][hapmap]
rs9871024	0.94[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9881860	1.00[ASN][1000 genomes]
rs9883000	0.94[CEU][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6797299	AMT	cis	Thyroid	GTEx
rs6797299	WDR6	cis	Muscle Skeletal	GTEx
rs6797299	RNF123	cis	Artery Tibial	GTEx
rs6797299	AMT	cis	lung	GTEx
rs6797299	AMT	cis	Nerve Tibial	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49596000-49615000	Weak transcription	Brain Germinal Matrix	brain
2	chr3:49596000-49616800	Weak transcription	Fetal Brain Female	brain
3	chr3:49601200-49612200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:49608600-49615600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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