Variant report

Variant	rs2312573
Chromosome Location	chr1:67172148-67172149
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10789216	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10889647	0.86[ASN][1000 genomes]
rs10889649	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11208948	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11208951	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11811699	0.82[EUR][1000 genomes]
rs12063436	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12119578	0.83[AMR][1000 genomes]
rs12138266	0.83[AMR][1000 genomes]
rs1325268	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1408852	0.86[ASN][1000 genomes]
rs1498354	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1547644	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16844	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2016093	0.82[AMR][1000 genomes]
rs2181625	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2274987	0.81[AMR][1000 genomes]
rs3738167	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs489300	0.88[ASN][1000 genomes]
rs650202	0.88[ASN][1000 genomes]
rs6588216	0.84[EUR][1000 genomes]
rs6659325	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6663604	0.82[AMR][1000 genomes]
rs6679379	0.84[AMR][1000 genomes]
rs682896	0.88[ASN][1000 genomes]
rs7512401	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7528346	0.84[EUR][1000 genomes]
rs7541249	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869413	chr1:67082512-67414286	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv3430238	chr1:67171264-67173162	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2312573	TCTEX1D1	cis	Whole Blood	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67155800-67177200	Weak transcription	Brain Anterior Caudate	brain
2	chr1:67156000-67177200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:67156800-67191400	Weak transcription	Fetal Brain Female	brain
4	chr1:67157000-67208800	Weak transcription	Brain Germinal Matrix	brain
5	chr1:67157200-67189600	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:67157400-67191600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:67158200-67189400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr1:67158400-67191400	Weak transcription	Left Ventricle	heart
9	chr1:67158600-67189400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:67160400-67189400	Weak transcription	Brain Angular Gyrus	brain
11	chr1:67165200-67191400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:67165400-67187600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:67165400-67191600	Weak transcription	Aorta	Aorta
14	chr1:67165400-67206800	Weak transcription	Fetal Brain Male	brain
15	chr1:67168000-67185000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:67170200-67186800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:67171400-67189400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:67171400-67198000	Weak transcription	NHLF	lung

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