Variant report

Variant	rs12340301
Chromosome Location	chr9:14979866-14979867
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10114147	0.88[EUR][1000 genomes]
rs10756632	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10810294	0.88[ASN][1000 genomes]
rs10810295	0.89[ASN][1000 genomes]
rs10810296	0.88[ASN][1000 genomes]
rs10810297	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10810298	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10810299	0.90[ASN][1000 genomes]
rs10810305	0.82[ASN][1000 genomes]
rs10810306	0.85[ASN][1000 genomes]
rs10810307	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10810308	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10961806	0.88[ASN][1000 genomes]
rs10961809	0.88[ASN][1000 genomes]
rs10961811	0.81[EUR][1000 genomes]
rs10961814	0.94[ASN][1000 genomes]
rs10961817	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10961819	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10961820	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11515200	0.88[ASN][1000 genomes]
rs11793253	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12378196	0.89[ASN][1000 genomes]
rs12379705	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1357474	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1403560	0.88[ASN][1000 genomes]
rs1412720	0.88[EUR][1000 genomes]
rs1412724	0.81[EUR][1000 genomes]
rs1464607	0.81[EUR][1000 genomes]
rs1464608	0.88[EUR][1000 genomes]
rs1589666	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1829850	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1851590	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1855140	0.81[EUR][1000 genomes]
rs1880012	0.84[EUR][1000 genomes]
rs1880013	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2049291	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2049292	0.94[ASN][1000 genomes]
rs2140322	0.82[EUR][1000 genomes]
rs2140326	0.81[EUR][1000 genomes]
rs2381973	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3861706	0.88[ASN][1000 genomes]
rs4008009	0.87[EUR][1000 genomes]
rs4535838	0.87[EUR][1000 genomes]
rs4546746	0.90[ASN][1000 genomes]
rs4548277	0.84[EUR][1000 genomes]
rs4553007	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6415721	0.82[EUR][1000 genomes]
rs6474876	0.85[EUR][1000 genomes]
rs7018678	0.84[EUR][1000 genomes]
rs7020107	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7026072	0.88[EUR][1000 genomes]
rs7027560	0.81[EUR][1000 genomes]
rs7028104	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7028135	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7028702	0.91[EUR][1000 genomes]
rs7030516	0.83[EUR][1000 genomes]
rs7030620	0.82[EUR][1000 genomes]
rs7037967	0.85[EUR][1000 genomes]
rs7040712	0.84[EUR][1000 genomes]
rs7042782	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7043477	0.80[AMR][1000 genomes]
rs7046824	0.85[EUR][1000 genomes]
rs7048248	0.81[EUR][1000 genomes]
rs7048509	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7350286	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7350287	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7848747	0.86[EUR][1000 genomes]
rs7855093	0.85[EUR][1000 genomes]
rs7857763	0.82[EUR][1000 genomes]
rs9298710	0.87[EUR][1000 genomes]
rs9969815	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv613637	chr9:14524438-15011915	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv613647	chr9:14852141-15016475	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv892620	chr9:14922877-15086021	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv892621	chr9:14928013-15043692	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2761503	chr9:14960217-15049343	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv892622	chr9:14960217-15055607	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv972296	chr9:14978869-14982045	Weak transcription Enhancers Bivalent Enhancer	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12340301	RP11-54D18.2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14957600-14982400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:14973800-14991400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr9:14978600-14980600	Weak transcription	Fetal Stomach	stomach

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