Variant report

Variant	rs41904
Chromosome Location	chr7:117893106-117893107
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10247768	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10487392	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11542074	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11974039	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11983651	0.82[EUR][1000 genomes]
rs12154684	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1544583	0.86[EUR][1000 genomes]
rs1544584	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17140984	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17141053	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2215628	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2286863	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28260	0.90[EUR][1000 genomes]
rs33924981	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34010516	0.85[EUR][1000 genomes]
rs34019303	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35218902	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35485182	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41903	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41912	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41921	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41923	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41924	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41925	0.90[EUR][1000 genomes]
rs41930	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41931	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41936	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs41962	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41989	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4260839	0.83[EUR][1000 genomes]
rs45604739	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4730837	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61328879	0.81[EUR][1000 genomes]
rs62466471	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62466515	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62468297	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62469806	0.82[EUR][1000 genomes]
rs6942513	0.81[EUR][1000 genomes]
rs6960940	0.84[EUR][1000 genomes]
rs769435	0.81[EUR][1000 genomes]
rs7786233	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7801976	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9641593	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[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	nsv869971	chr7:117420583-118274149	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv889088	chr7:117744660-117913648	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv889089	chr7:117865940-117921267	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv889090	chr7:117865940-118067460	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41904	LSM8	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117891400-117893600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr7:117892200-117893200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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