Variant report

Variant	rs2548264
Chromosome Location	chr5:100135574-100135575
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:100129066..100130718-chr5:100133106..100136007,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10057237	0.82[JPT][hapmap]
rs10059953	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10060686	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10072493	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10072498	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10075853	0.81[JPT][hapmap]
rs10478599	0.81[JPT][hapmap]
rs11584	0.84[EUR][1000 genomes]
rs11745097	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13358607	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13360613	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13857	0.82[JPT][hapmap]
rs149895	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs157042	0.91[ASN][1000 genomes]
rs157043	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs157181	0.91[ASN][1000 genomes]
rs17778837	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2544920	0.80[CHB][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2548256	0.84[EUR][1000 genomes]
rs2548261	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548262	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2548265	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2548274	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548280	0.84[EUR][1000 genomes]
rs2561520	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2725124	0.84[EUR][1000 genomes]
rs276456	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs276457	0.98[ASN][1000 genomes]
rs276458	0.91[ASN][1000 genomes]
rs276459	0.91[ASN][1000 genomes]
rs276460	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs276461	0.91[ASN][1000 genomes]
rs276462	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs276465	0.94[ASN][1000 genomes]
rs277863	0.86[ASN][1000 genomes]
rs277864	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277865	0.89[ASN][1000 genomes]
rs277866	0.89[ASN][1000 genomes]
rs277867	0.89[ASN][1000 genomes]
rs277868	0.90[ASN][1000 genomes]
rs277869	0.97[ASN][1000 genomes]
rs277870	0.92[ASN][1000 genomes]
rs277871	0.99[ASN][1000 genomes]
rs277872	0.99[ASN][1000 genomes]
rs278493	0.89[ASN][1000 genomes]
rs278494	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs278495	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs278496	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs278497	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs278498	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs278499	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs278500	0.89[ASN][1000 genomes]
rs278501	0.98[ASN][1000 genomes]
rs278502	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs278503	0.98[ASN][1000 genomes]
rs278504	0.98[ASN][1000 genomes]
rs3776155	0.82[JPT][hapmap]
rs3843478	0.82[JPT][hapmap]
rs3846626	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4702990	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4703115	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4703116	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703117	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4703118	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4703119	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4703126	0.82[JPT][hapmap]
rs55817847	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56165696	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57055845	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6595465	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6864315	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6883673	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6886392	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7710701	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7721627	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7736024	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9763775	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021183	chr5:99625857-100221426	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	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
3	esv2762532	chr5:100041758-100136552	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2548264	ST8SIA4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100114000-100136400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:100134400-100136000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:100134400-100139200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr5:100135400-100139000	Weak transcription	Brain Hippocampus Middle	brain

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