Variant report

Variant	rs2171642
Chromosome Location	chr12:48635390-48635391
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1021313	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10431526	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10437919	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10437920	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10467101	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10783234	0.81[ASN][1000 genomes]
rs10875762	0.83[ASN][1000 genomes]
rs10875764	0.80[ASN][1000 genomes]
rs10875767	0.93[ASN][1000 genomes]
rs10875768	0.91[ASN][1000 genomes]
rs10875769	0.89[ASN][1000 genomes]
rs10875770	0.93[ASN][1000 genomes]
rs10875772	0.95[ASN][1000 genomes]
rs10875777	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10875778	0.97[ASN][1000 genomes]
rs10875779	0.97[ASN][1000 genomes]
rs10875782	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875792	0.90[ASN][1000 genomes]
rs10875793	0.90[ASN][1000 genomes]
rs11168450	0.80[ASN][1000 genomes]
rs11168459	0.93[ASN][1000 genomes]
rs11168483	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168487	0.97[ASN][1000 genomes]
rs11168493	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168508	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11168510	0.91[ASN][1000 genomes]
rs11168514	0.90[ASN][1000 genomes]
rs11168516	0.90[ASN][1000 genomes]
rs11558768	0.82[ASN][1000 genomes]
rs12227601	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12300647	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12305511	0.85[ASN][1000 genomes]
rs12305647	0.85[ASN][1000 genomes]
rs12317751	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12318705	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122812	0.93[ASN][1000 genomes]
rs2012773	0.80[ASN][1000 genomes]
rs2279464	0.90[ASN][1000 genomes]
rs2409005	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2898065	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2898066	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760622	0.85[ASN][1000 genomes]
rs4760625	0.92[ASN][1000 genomes]
rs4760695	0.85[ASN][1000 genomes]
rs4760696	0.80[ASN][1000 genomes]
rs4760699	0.95[ASN][1000 genomes]
rs61940962	0.93[ASN][1000 genomes]
rs61941003	0.97[ASN][1000 genomes]
rs61941006	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7135779	0.80[ASN][1000 genomes]
rs716553	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7297298	0.92[ASN][1000 genomes]
rs7302466	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303055	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7486008	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7975956	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9634261	0.82[AMR][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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2171642	RP1-228P16.1	cis	Thyroid	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48612200-48635600	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:48630600-48636600	Weak transcription	Primary monocytes fromperipheralblood	blood

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