Variant report

Variant	rs13166819
Chromosome Location	chr5:50152860-50152861
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10052372	0.90[EUR][1000 genomes]
rs11950506	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11952107	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11954064	0.94[AMR][1000 genomes]
rs11955651	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11955934	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11959326	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13155662	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13156735	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13157079	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13159045	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13159239	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13161225	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13162738	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13163470	0.94[EUR][1000 genomes]
rs13163802	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13169153	0.94[EUR][1000 genomes]
rs13174498	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13176737	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13181031	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13181117	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13183910	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13186653	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13189183	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13190144	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16886309	0.94[EUR][1000 genomes]
rs34183555	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34264957	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34414061	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34677483	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34758774	0.85[EUR][1000 genomes]
rs34827507	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34855203	0.81[EUR][1000 genomes]
rs35128589	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35347195	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35473824	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41270305	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6859621	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6880398	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6883701	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6888271	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6888315	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71615978	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71615981	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71615983	0.94[EUR][1000 genomes]
rs71615984	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71615986	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71615988	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71615990	0.98[EUR][1000 genomes]
rs71615991	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7717073	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7726225	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7733931	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462159	chr5:49960673-50229851	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv598108	chr5:49960673-50229851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv598116	chr5:50064292-50318550	Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13166819	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50147600-50153600	Enhancers	Primary B cells from cord blood	blood
2	chr5:50147800-50153600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr5:50148200-50153800	Enhancers	Primary B cells from peripheral blood	blood
4	chr5:50150200-50153600	Enhancers	Fetal Brain Male	brain
5	chr5:50151600-50153400	Enhancers	Fetal Thymus	thymus
6	chr5:50152000-50153200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr5:50152200-50153000	Enhancers	GM12878-XiMat	blood
8	chr5:50152400-50153200	Enhancers	Brain Hippocampus Middle	brain
9	chr5:50152400-50153200	Enhancers	Dnd41	blood
10	chr5:50152400-50153400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr5:50152600-50153000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr5:50152800-50153400	Enhancers	Primary T helper cells fromperipheralblood	blood

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