Variant report

Variant	rs3870341
Chromosome Location	chr3:49584745-49584746
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49576405..49578999-chr3:49581800..49584941,3	K562	blood:
2	chr3:49576824..49578736-chr3:49583122..49584807,2	MCF-7	breast:
3	chr3:49582614..49585275-chr3:49588937..49591341,2	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1009051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10155014	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865956	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1106620	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11130204	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11130211	1.00[CHB][hapmap]
rs11715060	0.82[AFR][1000 genomes]
rs11719762	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs11720657	0.83[CEU][hapmap]
rs11928090	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13096474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13322887	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1352889	1.00[CHB][hapmap]
rs1464569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491983	1.00[CHB][hapmap]
rs1982861	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2177268	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs2312462	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329025	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3448	1.00[CEU][hapmap]
rs34890793	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs3866330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870339	0.90[CEU][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3905330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4052546	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855833	1.00[CHB][hapmap]
rs4855837	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4855853	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4855858	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855869	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs56049603	0.84[EUR][1000 genomes]
rs56127630	0.82[EUR][1000 genomes]
rs56324858	0.81[EUR][1000 genomes]
rs57273516	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259933	0.86[EUR][1000 genomes]
rs62259943	0.80[EUR][1000 genomes]
rs62259947	0.82[EUR][1000 genomes]
rs62261183	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62261249	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6446275	0.86[EUR][1000 genomes]
rs6769744	1.00[ASN][1000 genomes]
rs6774202	1.00[CHB][hapmap]
rs6783003	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs6785045	0.82[EUR][1000 genomes]
rs6805609	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs72934271	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73088137	0.83[EUR][1000 genomes]
rs7355800	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7374731	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7613491	0.90[EUR][1000 genomes]
rs7619789	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620024	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622786	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7625857	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7644148	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7647973	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs7648995	0.82[EUR][1000 genomes]
rs7651372	0.90[EUR][1000 genomes]
rs7653505	1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs8897	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs940045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9654010	0.84[EUR][1000 genomes]
rs974495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs9757181	0.95[CEU][hapmap]
rs9809237	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9817807	0.80[EUR][1000 genomes]
rs9842132	0.80[EUR][1000 genomes]
rs9860055	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9861027	0.82[EUR][1000 genomes]
rs9862534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871024	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs3870341	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs3870341	AMT	cis	Whole Blood	GTEx
rs3870341	WDR6	cis	lung	GTEx
rs3870341	NICN1-AS1	cis	Thyroid	GTEx
rs3870341	AMT	cis	Esophagus Muscularis	GTEx
rs3870341	NICN1	cis	Thyroid	GTEx
rs3870341	WDR6	cis	Esophagus Muscularis	GTEx
rs3870341	WDR6	cis	Muscle Skeletal	GTEx
rs3870341	AMT	cis	Esophagus Mucosa	GTEx
rs3870341	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs3870341	AMT	cis	Artery Tibial	GTEx
rs3870341	AMT	cis	Thyroid	GTEx
rs3870341	AMT	cis	lung	GTEx
rs3870341	AMT	cis	Adipose Subcutaneous	GTEx
rs3870341	AMT	cis	Muscle Skeletal	GTEx
rs3870341	WDR6	cis	Nerve Tibial	GTEx
rs3870341	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs3870341	AMT	cis	Nerve Tibial	GTEx
rs3870341	AMT	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49581800-49585000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:49584400-49585200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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