Variant report

Variant	rs10478649
Chromosome Location	chr5:100271669-100271670
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10035529	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10043056	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10058901	0.89[EUR][1000 genomes]
rs10059470	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10059846	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10069305	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10214216	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10477661	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10478633	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10515303	0.88[EUR][1000 genomes]
rs11241752	0.81[EUR][1000 genomes]
rs11241755	0.81[EUR][1000 genomes]
rs11241794	0.87[EUR][1000 genomes]
rs11584	0.84[EUR][1000 genomes]
rs11742480	0.80[AMR][1000 genomes]
rs11742504	0.80[AMR][1000 genomes]
rs13354021	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13355889	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1423380	0.89[EUR][1000 genomes]
rs1428439	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17725452	0.81[EUR][1000 genomes]
rs17725678	0.81[EUR][1000 genomes]
rs17726244	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17726346	0.87[EUR][1000 genomes]
rs17782041	0.81[EUR][1000 genomes]
rs17782250	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1820150	0.85[EUR][1000 genomes]
rs1833862	0.81[EUR][1000 genomes]
rs2400313	0.81[EUR][1000 genomes]
rs2544913	0.82[EUR][1000 genomes]
rs2544920	0.84[EUR][1000 genomes]
rs2548256	0.84[EUR][1000 genomes]
rs2548276	0.85[EUR][1000 genomes]
rs2548278	0.85[EUR][1000 genomes]
rs2548280	0.84[EUR][1000 genomes]
rs2725116	0.85[EUR][1000 genomes]
rs2725124	0.84[EUR][1000 genomes]
rs34564041	0.88[EUR][1000 genomes]
rs3756351	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3756352	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3756353	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3756354	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3756355	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3776170	0.88[EUR][1000 genomes]
rs3776171	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3776174	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3776176	0.89[EUR][1000 genomes]
rs4703131	0.81[EUR][1000 genomes]
rs4703133	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55805984	0.87[EUR][1000 genomes]
rs55861847	0.88[EUR][1000 genomes]
rs55959219	0.81[EUR][1000 genomes]
rs55968003	0.85[EUR][1000 genomes]
rs56752243	0.88[EUR][1000 genomes]
rs59030588	0.88[EUR][1000 genomes]
rs60663279	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60853907	0.90[EUR][1000 genomes]
rs6893927	0.94[ASN][1000 genomes]
rs72778635	0.82[EUR][1000 genomes]
rs72778649	0.87[EUR][1000 genomes]
rs72778650	0.85[EUR][1000 genomes]
rs7703643	0.88[EUR][1000 genomes]
rs7737721	0.86[EUR][1000 genomes]
rs966257	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023765	chr5:99915011-100733755	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	esv1834675	chr5:100143084-100535029	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv882471	chr5:100234439-100362071	Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv882472	chr5:100234439-100512338	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv462320	chr5:100247554-100775607	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv599176	chr5:100247554-100775607	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv882473	chr5:100263707-100532885	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv882474	chr5:100263707-100537863	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv524773	chr5:100264350-100309166	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv525359	chr5:100264350-100349324	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10478649	ST8SIA4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100270400-100276000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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