Variant report

Variant	rs406288
Chromosome Location	chr5:54298590-54298591
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1035408	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12659978	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1517208	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1517210	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs154039	0.86[EUR][1000 genomes]
rs154040	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1593953	0.87[AMR][1000 genomes]
rs164251	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs164253	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs171181	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs173903	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1820056	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs182987	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1845290	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs190453	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2416282	0.81[AMR][1000 genomes]
rs2431548	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2434664	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2434665	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs255856	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs255858	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs255863	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs255867	0.82[EUR][1000 genomes]
rs255874	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs26960	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs26983	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs26985	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs26987	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs26988	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs27566	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs27700	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2910018	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2914252	0.81[AMR][1000 genomes]
rs34075952	0.81[AMR][1000 genomes]
rs348927	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs348933	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs348936	0.82[AMR][1000 genomes]
rs348949	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs348950	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs348953	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs348959	0.89[AMR][1000 genomes]
rs36612	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3857435	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3857437	0.82[AMR][1000 genomes]
rs423089	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4235796	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4415069	0.81[EUR][1000 genomes]
rs4438867	0.82[EUR][1000 genomes]
rs4444963	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs459428	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs461034	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs463216	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4639215	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs465898	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs466564	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4705813	0.80[EUR][1000 genomes]
rs57617774	0.82[EUR][1000 genomes]
rs62373764	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6594711	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6594736	0.82[EUR][1000 genomes]
rs675353	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6869097	0.86[AFR][1000 genomes]
rs7702120	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7713348	0.81[AMR][1000 genomes]
rs7713378	0.82[EUR][1000 genomes]
rs7730802	0.82[AMR][1000 genomes]
rs9326895	0.80[EUR][1000 genomes]
rs9686772	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830301	chr5:54225874-54423505	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54286400-54300000	Weak transcription	Primary T cells from cord blood	blood
2	chr5:54287600-54302600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr5:54287800-54299400	Weak transcription	NHLF	lung
4	chr5:54293400-54299000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:54293600-54299000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr5:54297400-54303000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr5:54297600-54298600	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr5:54297800-54298600	Enhancers	Dnd41	blood
9	chr5:54297800-54300200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr5:54298000-54299000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:54298000-54299000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr5:54298000-54300200	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr5:54298000-54300600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr5:54298200-54302200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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