Variant report

Variant	rs9425339
Chromosome Location	chr1:184647382-184647383
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1040666	0.84[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1046239	0.84[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10752941	0.81[ASN][1000 genomes]
rs10797987	0.87[ASN][1000 genomes]
rs10911631	0.84[EUR][1000 genomes]
rs10911640	0.84[ASN][1000 genomes]
rs10911644	0.91[CEU][hapmap]
rs10911645	0.84[CEU][hapmap]
rs11808675	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12043236	0.83[ASN][1000 genomes]
rs12071631	0.84[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs12124929	0.87[CEU][hapmap]
rs12131285	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs12137438	0.84[EUR][1000 genomes]
rs12567225	0.92[CEU][hapmap]
rs12567226	0.92[CEU][hapmap]
rs2024765	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2024767	0.83[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2064605	0.92[CEU][hapmap]
rs2207733	0.83[ASN][1000 genomes]
rs2333715	0.92[CEU][hapmap]
rs2333716	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2877994	0.83[EUR][1000 genomes]
rs3736757	0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs3895196	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs4469687	0.83[ASN][1000 genomes]
rs4498770	0.83[ASN][1000 genomes]
rs4651230	0.91[CEU][hapmap]
rs6663178	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs6677073	0.85[ASN][1000 genomes]
rs7523023	0.83[ASN][1000 genomes]
rs7525074	0.83[ASN][1000 genomes]
rs861575	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs861577	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9425338	0.85[EUR][1000 genomes]
rs9425340	0.84[EUR][1000 genomes]
rs9425341	0.81[ASN][1000 genomes]
rs9425343	0.92[CEU][hapmap]
rs9425632	0.84[EUR][1000 genomes]
rs9425633	0.83[ASN][1000 genomes]
rs9658937	0.84[ASN][1000 genomes]
rs9661314	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv832037	chr1:184568194-184756597	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9425339	EDEM3	Cis_1M	lymphoblastoid	RTeQTL
rs9425339	EDEM3	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184641400-184672800	Weak transcription	Gastric	stomach

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