Variant report

Variant	rs12438312
Chromosome Location	chr15:83363323-83363324
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:83363148..83365417-chr15:83367537..83371581,3	K562	blood:

Variant related genes	Relation type
ENSG00000103723	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10400906	0.94[ASN][1000 genomes]
rs10468217	0.87[ASN][1000 genomes]
rs10906984	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1145172	0.83[ASN][1000 genomes]
rs1145173	0.83[ASN][1000 genomes]
rs11631963	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11633829	0.93[ASN][1000 genomes]
rs11635624	0.84[ASN][1000 genomes]
rs11637433	0.95[ASN][1000 genomes]
rs11855735	0.92[ASN][1000 genomes]
rs12148332	0.89[ASN][1000 genomes]
rs12438334	0.89[AFR][1000 genomes]
rs12442686	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1259180	0.88[ASN][1000 genomes]
rs1259182	0.92[ASN][1000 genomes]
rs1259183	0.91[ASN][1000 genomes]
rs1267657	0.84[ASN][1000 genomes]
rs1267658	0.83[ASN][1000 genomes]
rs1267659	0.83[ASN][1000 genomes]
rs1269134	0.93[ASN][1000 genomes]
rs12911134	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12916980	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1313492	0.91[ASN][1000 genomes]
rs1313493	0.91[ASN][1000 genomes]
rs1367841	0.95[ASN][1000 genomes]
rs1594511	0.95[ASN][1000 genomes]
rs17158390	0.94[ASN][1000 genomes]
rs1864699	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2099259	0.95[ASN][1000 genomes]
rs2278355	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2567635	0.90[ASN][1000 genomes]
rs2567636	0.89[ASN][1000 genomes]
rs2678445	0.84[ASN][1000 genomes]
rs2678448	0.89[ASN][1000 genomes]
rs28374463	0.90[ASN][1000 genomes]
rs28415133	0.88[ASN][1000 genomes]
rs28595450	0.89[AFR][1000 genomes]
rs28667458	0.93[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2870965	0.90[ASN][1000 genomes]
rs2870966	0.94[ASN][1000 genomes]
rs28808991	0.90[ASN][1000 genomes]
rs34186444	0.94[ASN][1000 genomes]
rs35934048	0.85[ASN][1000 genomes]
rs36109438	0.88[ASN][1000 genomes]
rs3970696	0.89[ASN][1000 genomes]
rs4778686	0.95[ASN][1000 genomes]
rs4779032	0.88[ASN][1000 genomes]
rs4779039	0.87[ASN][1000 genomes]
rs4779041	0.95[ASN][1000 genomes]
rs4779044	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4779050	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4779053	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4779054	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs55924160	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57181760	0.93[ASN][1000 genomes]
rs6603033	0.95[ASN][1000 genomes]
rs698500	0.86[ASN][1000 genomes]
rs7165125	0.92[ASN][1000 genomes]
rs7166248	0.90[ASN][1000 genomes]
rs7167880	0.94[ASN][1000 genomes]
rs7171180	0.95[ASN][1000 genomes]
rs7178350	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7181761	0.87[ASN][1000 genomes]
rs7182403	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7183881	0.96[ASN][1000 genomes]
rs7184045	0.84[AFR][1000 genomes]
rs7494860	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7496954	0.96[ASN][1000 genomes]
rs783520	0.93[ASN][1000 genomes]
rs783521	0.94[ASN][1000 genomes]
rs783522	0.94[ASN][1000 genomes]
rs783523	0.94[ASN][1000 genomes]
rs783525	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs783526	0.93[ASN][1000 genomes]
rs783527	0.93[ASN][1000 genomes]
rs783529	0.89[ASN][1000 genomes]
rs783530	0.89[ASN][1000 genomes]
rs783531	0.88[ASN][1000 genomes]
rs783532	0.90[ASN][1000 genomes]
rs783533	0.91[ASN][1000 genomes]
rs783534	0.91[ASN][1000 genomes]
rs783535	0.88[ASN][1000 genomes]
rs783536	0.90[ASN][1000 genomes]
rs783537	0.87[ASN][1000 genomes]
rs783539	0.89[ASN][1000 genomes]
rs783540	0.90[ASN][1000 genomes]
rs783543	0.81[ASN][1000 genomes]
rs783545	0.87[ASN][1000 genomes]
rs803687	0.81[ASN][1000 genomes]
rs803688	0.83[ASN][1000 genomes]
rs803747	0.90[ASN][1000 genomes]
rs8040293	0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs8043401	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9652567	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054171	chr15:83237514-83468077	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1036950	chr15:83245326-83461261	Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1036462	chr15:83245326-83472507	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv34318	chr15:83283555-83453495	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv1039021	chr15:83283994-83431548	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv3493740	chr15:83295897-83458896	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	esv3493739	chr15:83296247-83458846	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
8	esv3493738	chr15:83296905-83457854	Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	esv3493742	chr15:83296993-83457792	Weak transcription Active TSS Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
10	nsv817702	chr15:83299461-83457424	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	esv3443566	chr15:83346946-83367664	Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv904450	chr15:83347193-83395340	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12438312	RPS17	Cis_1M	lymphoblastoid	RTeQTL
rs12438312	RP13-996F3.5	cis	Esophagus Mucosa	GTEx
rs12438312	RP11-152F13.8	cis	Esophagus Mucosa	GTEx
rs12438312	LOC402057///RPS17	trans	lymphoblastoid	RTeQTL
rs12438312	GOLGA6L10	cis	Esophagus Mucosa	GTEx
rs12438312	FLJ40113///LOC161527///LOC440295///LOC642346	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83349800-83377200	Weak transcription	Brain Anterior Caudate	brain
2	chr15:83350400-83368000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:83350400-83369800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:83350400-83372800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:83350600-83368400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr15:83350600-83369000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr15:83351600-83377200	Weak transcription	Brain Hippocampus Middle	brain
8	chr15:83351800-83377200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:83351800-83377400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:83355600-83368600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:83357600-83368200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:83357800-83367800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr15:83357800-83368800	Weak transcription	Brain Angular Gyrus	brain
14	chr15:83358000-83365400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr15:83358200-83377200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:83358400-83366400	Weak transcription	Brain Germinal Matrix	brain
17	chr15:83358400-83367600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr15:83358600-83367600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr15:83361400-83366200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:83361600-83364200	Weak transcription	Fetal Brain Female	brain
21	chr15:83363000-83370400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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