Variant report

Variant	rs9859178
Chromosome Location	chr3:51236652-51236653
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 126 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10212240	0.85[AMR][1000 genomes]
rs10212250	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11130274	0.87[AMR][1000 genomes]
rs11130282	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11712871	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11919932	0.83[AMR][1000 genomes]
rs12630889	0.83[AMR][1000 genomes]
rs2355934	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28470684	0.83[AMR][1000 genomes]
rs28670710	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4130474	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4244697	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4244700	0.83[AMR][1000 genomes]
rs4244701	0.83[AMR][1000 genomes]
rs4244702	0.83[AMR][1000 genomes]
rs4244703	0.83[AMR][1000 genomes]
rs4244704	0.83[AMR][1000 genomes]
rs4263323	0.83[AMR][1000 genomes]
rs4267674	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4269109	0.83[AMR][1000 genomes]
rs4286453	0.83[AMR][1000 genomes]
rs4293735	0.87[AMR][1000 genomes]
rs4301044	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4308313	0.96[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4309762	0.83[AMR][1000 genomes]
rs4309763	0.83[AMR][1000 genomes]
rs4317135	0.83[AMR][1000 genomes]
rs4328835	0.91[AMR][1000 genomes]
rs4340738	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4359843	0.87[AMR][1000 genomes]
rs4367101	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4377512	0.83[AMR][1000 genomes]
rs4378999	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4390967	0.83[AMR][1000 genomes]
rs4422345	0.81[AMR][1000 genomes]
rs4444745	0.83[AMR][1000 genomes]
rs4446244	0.83[AMR][1000 genomes]
rs4453876	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4464493	0.83[AMR][1000 genomes]
rs4465974	0.83[AMR][1000 genomes]
rs4478114	0.83[AMR][1000 genomes]
rs4487270	0.83[AMR][1000 genomes]
rs4488874	0.83[AMR][1000 genomes]
rs4491946	0.83[AMR][1000 genomes]
rs4505743	0.83[AMR][1000 genomes]
rs4507294	0.83[AMR][1000 genomes]
rs4511930	0.83[AMR][1000 genomes]
rs4511933	0.83[AMR][1000 genomes]
rs4528983	0.96[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4530566	0.83[AMR][1000 genomes]
rs4532165	0.87[AMR][1000 genomes]
rs4549311	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4568176	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4568177	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4582086	0.83[AMR][1000 genomes]
rs4589968	0.83[AMR][1000 genomes]
rs4613496	0.83[AMR][1000 genomes]
rs4615113	0.83[AMR][1000 genomes]
rs4927957	0.81[AMR][1000 genomes]
rs4927958	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4927959	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4927964	0.87[AMR][1000 genomes]
rs4927965	0.87[AMR][1000 genomes]
rs4927967	0.91[AMR][1000 genomes]
rs4927971	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4927972	0.96[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4927977	0.83[AMR][1000 genomes]
rs4927978	0.83[AMR][1000 genomes]
rs4927979	0.83[AMR][1000 genomes]
rs4927982	0.83[AMR][1000 genomes]
rs4927983	0.83[AMR][1000 genomes]
rs4927984	0.83[AMR][1000 genomes]
rs6445393	0.91[AMR][1000 genomes]
rs6445455	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6445551	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6445750	0.83[AMR][1000 genomes]
rs6445779	0.83[AMR][1000 genomes]
rs6446011	0.83[AMR][1000 genomes]
rs6446118	0.83[AMR][1000 genomes]
rs6446167	0.87[AMR][1000 genomes]
rs6446168	0.87[AMR][1000 genomes]
rs6763136	0.96[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6767329	0.83[AMR][1000 genomes]
rs6769957	0.87[AMR][1000 genomes]
rs6772664	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6775483	0.87[AMR][1000 genomes]
rs6777719	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6779658	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6780575	0.85[AMR][1000 genomes]
rs6787773	0.83[AMR][1000 genomes]
rs6793613	0.83[AMR][1000 genomes]
rs6793648	0.83[AMR][1000 genomes]
rs6797368	0.91[AMR][1000 genomes]
rs6799211	0.83[AMR][1000 genomes]
rs6803672	0.91[AMR][1000 genomes]
rs6806090	0.83[AMR][1000 genomes]
rs6808206	0.83[AMR][1000 genomes]
rs6809080	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7611873	0.83[AMR][1000 genomes]
rs7615291	0.83[AMR][1000 genomes]
rs7619584	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7628533	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7629433	0.83[AMR][1000 genomes]
rs7630616	0.85[AMR][1000 genomes]
rs7630730	0.85[AMR][1000 genomes]
rs7639161	0.83[AMR][1000 genomes]
rs7640263	0.83[AMR][1000 genomes]
rs7644957	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7652655	0.83[AMR][1000 genomes]
rs7652818	0.83[AMR][1000 genomes]
rs7653451	0.83[AMR][1000 genomes]
rs9827072	0.83[AMR][1000 genomes]
rs9828200	0.83[AMR][1000 genomes]
rs9839860	0.87[AMR][1000 genomes]
rs9841339	0.87[AMR][1000 genomes]
rs9850021	0.83[AMR][1000 genomes]
rs9858412	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9864574	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9867256	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9869123	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9871539	0.87[AMR][1000 genomes]
rs9883739	0.93[AMR][1000 genomes];0.88[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
rs9859178	TEX264	cis	Esophagus Muscularis	GTEx

Chromatin state (count:11 , 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	chr3:51234600-51262800	Weak transcription	Brain Angular Gyrus	brain
5	chr3:51235400-51252400	Weak transcription	Brain Anterior Caudate	brain
6	chr3:51235800-51285000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:51236600-51237000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:51236600-51237000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:51236600-51237200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:51236600-51251800	Weak transcription	Fetal Brain Female	brain
11	chr3:51236600-51265000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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