Variant report

Variant	rs9864574
Chromosome Location	chr3:51235784-51235785
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 163 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:159)

rs_ID	r²[population]
rs10212240	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10212250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130273	0.82[AFR][1000 genomes]
rs11130274	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919932	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12630889	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1383252	0.88[EUR][1000 genomes]
rs1480363	0.88[EUR][1000 genomes]
rs1480365	0.82[EUR][1000 genomes]
rs2061951	0.88[EUR][1000 genomes]
rs2355934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2355941	0.88[EUR][1000 genomes]
rs2355942	0.88[EUR][1000 genomes]
rs28470684	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28670710	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4130474	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4244697	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4244699	0.82[AFR][1000 genomes]
rs4244700	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4244701	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4244702	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4244703	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4244704	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4244705	0.81[AMR][1000 genomes]
rs4263323	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4267674	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4269109	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4286453	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4289378	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4293735	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4301044	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4308313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4309762	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4309763	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4317135	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4328835	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4340738	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4359843	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4367101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4377512	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4378999	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4390967	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4422345	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4438692	0.82[AFR][1000 genomes]
rs4444745	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4446244	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4453876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4464493	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4465974	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4478114	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4487270	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4488874	0.87[AMR][1000 genomes]
rs4491946	0.87[AMR][1000 genomes]
rs4505743	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4507294	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4511933	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4528983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4530566	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4532165	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4541436	0.82[AFR][1000 genomes]
rs4549311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4568176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4568177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4574329	0.82[AFR][1000 genomes]
rs4582086	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4589968	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4613496	0.87[AMR][1000 genomes]
rs4615113	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4927957	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4927958	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4927959	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4927960	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4927964	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4927965	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4927967	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4927971	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4927972	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4927976	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4927977	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4927978	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4927979	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4927980	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4927982	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4927983	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4927984	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4927986	0.82[ASN][1000 genomes]
rs4974095	0.82[EUR][1000 genomes]
rs60866608	0.88[AFR][1000 genomes]
rs6445393	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6445455	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6445551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445600	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6445717	0.82[AFR][1000 genomes]
rs6445750	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6445779	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6446011	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6446118	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6446167	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6446168	0.91[AMR][1000 genomes]
rs6763136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6767329	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6768601	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6769957	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6772664	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6775483	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6777719	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6779658	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6780575	0.89[AMR][1000 genomes]
rs6782946	0.82[EUR][1000 genomes]
rs6785558	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6787773	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6793613	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6793648	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6797368	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6799211	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6800805	0.82[EUR][1000 genomes]
rs6803672	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6806090	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6808206	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6809080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809524	0.94[AFR][1000 genomes]
rs73833999	0.88[AFR][1000 genomes]
rs7610901	0.82[AFR][1000 genomes]
rs7611873	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7614785	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7615291	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7619584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629433	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7630616	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7630730	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7634514	0.82[EUR][1000 genomes]
rs7639161	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7640263	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7643781	0.82[ASN][1000 genomes]
rs7644957	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7652655	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7652818	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7653451	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7653539	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs922612	0.88[EUR][1000 genomes]
rs9284887	0.82[AFR][1000 genomes]
rs9284888	0.82[AFR][1000 genomes]
rs9713241	0.82[AFR][1000 genomes]
rs9827072	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9828200	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9839860	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9841339	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9850021	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9857727	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9858412	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859178	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9867256	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9869123	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871539	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9878100	0.82[EUR][1000 genomes]
rs9883739	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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	nsv491647	chr3:50856276-51245158	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats 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 target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9864574	TEX264	cis	Esophagus Muscularis	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51213000-51246000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:51227200-51250600	Weak transcription	Brain Hippocampus Middle	brain
3	chr3:51228200-51252400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:51234600-51235800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:51234600-51236600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
6	chr3:51234600-51236600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:51234600-51262800	Weak transcription	Brain Angular Gyrus	brain
8	chr3:51234800-51236600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:51235000-51236600	ZNF genes & repeats	Fetal Brain Female	brain
10	chr3:51235400-51236600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
11	chr3:51235400-51252400	Weak transcription	Brain Anterior Caudate	brain
12	chr3:51235600-51236400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
13	chr3:51235600-51236600	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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