Variant report

Variant	rs277869
Chromosome Location	chr5:100112636-100112637
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10059953	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10060686	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10072493	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10072498	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11745097	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13358607	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13360613	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs149895	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs157042	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs157043	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs157181	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17778837	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2544920	0.82[ASN][1000 genomes]
rs2548261	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2548262	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2548264	0.97[ASN][1000 genomes]
rs2548265	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2548274	0.97[ASN][1000 genomes]
rs2561520	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs276456	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs276457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs276458	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs276459	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs276460	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs276461	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs276462	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs276465	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs277863	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs277864	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs277865	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs277866	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs277867	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs277868	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs277870	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs277871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs278493	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs278494	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs278495	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs278496	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs278497	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs278498	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs278499	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs278500	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs278501	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs278502	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs278503	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs278504	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs279105	0.82[EUR][1000 genomes]
rs3846626	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4702990	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4703115	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4703116	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4703117	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4703118	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4703119	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55817847	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56165696	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57055845	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6595465	0.86[ASN][1000 genomes]
rs6864315	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6883673	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6886392	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7710701	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7721627	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7736024	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9763775	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
rs277869	ST8SIA4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100109200-100113000	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr5:100109200-100113200	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr5:100109200-100113200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr5:100109200-100113200	Weak transcription	Fetal Kidney	kidney
5	chr5:100110800-100113600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr5:100111200-100113200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr5:100111200-100113400	Enhancers	Primary B cells from cord blood	blood
8	chr5:100111400-100113000	Enhancers	GM12878-XiMat	blood
9	chr5:100111400-100114400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr5:100111400-100114400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:100111400-100114800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr5:100111600-100113400	Weak transcription	Primary B cells from peripheral blood	blood
13	chr5:100111800-100113200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr5:100112000-100114000	Enhancers	HMEC	breast
15	chr5:100112200-100113000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:100112200-100113000	Enhancers	Dnd41	blood
17	chr5:100112200-100113200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:100112200-100113200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:100112200-100113200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr5:100112200-100113200	Weak transcription	A549	lung
21	chr5:100112200-100113200	Enhancers	HUVEC	blood vessel
22	chr5:100112200-100113200	Enhancers	Osteobl	bone
23	chr5:100112200-100113400	Enhancers	Hela-S3	cervix
24	chr5:100112200-100113400	Enhancers	NHEK	skin
25	chr5:100112200-100113800	Enhancers	NHLF	lung
26	chr5:100112200-100114000	Enhancers	NHDF-Ad	bronchial
27	chr5:100112400-100113200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr5:100112600-100113400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:100112600-100113400	Enhancers	Primary neutrophils fromperipheralblood	blood

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