Variant report

Variant	rs277866
Chromosome Location	chr5:100093544-100093545
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:100091660..100093864-chr5:100095640..100097485,2	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10059953	0.89[ASN][1000 genomes]
rs10060686	0.88[ASN][1000 genomes]
rs10072493	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10072498	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11745097	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13358607	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13360613	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs149895	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs157042	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs157043	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs157181	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17778837	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2548261	0.89[ASN][1000 genomes]
rs2548262	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2548264	0.89[ASN][1000 genomes]
rs2548274	0.89[ASN][1000 genomes]
rs2561520	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs276456	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs276457	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs276458	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs276459	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs276460	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs276461	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs276462	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs276465	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs277864	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs277865	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277867	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277868	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs277869	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs277870	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs277871	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs277872	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs278493	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs278494	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278495	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278496	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278497	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278498	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278499	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278500	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs278501	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278502	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278503	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278504	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs279105	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3846626	0.88[ASN][1000 genomes]
rs4702990	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4703115	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4703116	0.89[ASN][1000 genomes]
rs4703117	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4703118	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4703119	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55817847	0.87[ASN][1000 genomes]
rs56165696	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57055845	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6595465	0.89[ASN][1000 genomes]
rs6864315	0.90[ASN][1000 genomes]
rs6883673	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6886392	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7710701	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7721627	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7736024	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9763775	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][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	nsv948969	chr5:99534096-100133827	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	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
3	nsv1017420	chr5:99745775-100133140	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv537825	chr5:99745775-100133140	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	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
6	nsv882467	chr5:99952282-100100157	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv882470	chr5:100018392-100100157	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	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
9	nsv462319	chr5:100060150-100100157	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv599175	chr5:100060150-100100157	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs277866	ST8SIA4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100091200-100093800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:100092000-100096400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:100092400-100094800	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr5:100092600-100093600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
5	chr5:100092600-100093600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
6	chr5:100092600-100094400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:100092600-100094600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:100092800-100094600	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr5:100093000-100094600	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr5:100093000-100094600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
11	chr5:100093200-100093600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links