Variant report

Variant	rs12129052
Chromosome Location	chr1:169880635-169880636
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169862438..169864438-chr1:169879643..169881893,2	K562	blood:
2	chr1:169861921..169864438-chr1:169879643..169882504,3	K562	blood:
3	chr1:169861017..169866202-chr1:169878725..169885490,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000000457	Chromatin interaction

Extended variants
information (count: 277 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:269)

rs_ID	r²[population]
rs1046058	0.89[EUR][1000 genomes]
rs10489173	0.89[EUR][1000 genomes]
rs10489174	0.89[EUR][1000 genomes]
rs10489176	0.84[EUR][1000 genomes]
rs10800489	0.91[EUR][1000 genomes]
rs10919253	0.89[EUR][1000 genomes]
rs12045551	0.93[AFR][1000 genomes]
rs12116524	0.89[EUR][1000 genomes]
rs12116601	0.93[EUR][1000 genomes]
rs12116650	0.89[EUR][1000 genomes]
rs12117794	0.87[EUR][1000 genomes]
rs12118305	0.83[EUR][1000 genomes]
rs12118431	0.89[EUR][1000 genomes]
rs12118559	0.89[EUR][1000 genomes]
rs12118739	0.83[EUR][1000 genomes]
rs12119368	0.89[EUR][1000 genomes]
rs12119386	0.89[EUR][1000 genomes]
rs12119447	0.83[EUR][1000 genomes]
rs12119473	0.84[EUR][1000 genomes]
rs12119635	0.89[EUR][1000 genomes]
rs12119665	0.83[EUR][1000 genomes]
rs12120114	0.89[EUR][1000 genomes]
rs12120229	0.82[EUR][1000 genomes]
rs12120727	0.89[EUR][1000 genomes]
rs12121045	0.93[EUR][1000 genomes]
rs12121113	0.87[EUR][1000 genomes]
rs12121443	0.89[EUR][1000 genomes]
rs12121451	0.83[EUR][1000 genomes]
rs12121614	0.93[EUR][1000 genomes]
rs12121797	0.83[EUR][1000 genomes]
rs12122419	0.89[EUR][1000 genomes]
rs12122720	0.83[EUR][1000 genomes]
rs12122767	0.89[EUR][1000 genomes]
rs12122885	0.83[EUR][1000 genomes]
rs12123432	0.89[EUR][1000 genomes]
rs12123483	0.89[EUR][1000 genomes]
rs12123686	0.83[EUR][1000 genomes]
rs12123806	0.96[EUR][1000 genomes]
rs12123835	0.96[EUR][1000 genomes]
rs12123865	0.83[EUR][1000 genomes]
rs12124032	0.93[EUR][1000 genomes]
rs12124384	0.80[EUR][1000 genomes]
rs12124561	0.96[EUR][1000 genomes]
rs12124750	0.96[EUR][1000 genomes]
rs12124775	0.89[EUR][1000 genomes]
rs12124907	0.83[EUR][1000 genomes]
rs12125023	0.81[EUR][1000 genomes]
rs12125595	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12125679	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12126591	0.89[EUR][1000 genomes]
rs12127120	0.83[EUR][1000 genomes]
rs12127174	0.80[EUR][1000 genomes]
rs12127211	0.96[EUR][1000 genomes]
rs12127500	0.93[EUR][1000 genomes]
rs12127911	0.83[EUR][1000 genomes]
rs12128126	0.83[EUR][1000 genomes]
rs12128308	0.96[EUR][1000 genomes]
rs12128929	0.89[EUR][1000 genomes]
rs12129951	0.91[EUR][1000 genomes]
rs12130263	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12131192	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12131357	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12131444	0.89[EUR][1000 genomes]
rs12132173	0.83[EUR][1000 genomes]
rs12132222	0.88[EUR][1000 genomes]
rs12132384	0.89[EUR][1000 genomes]
rs12132633	0.83[EUR][1000 genomes]
rs12133074	0.89[EUR][1000 genomes]
rs12133108	0.91[EUR][1000 genomes]
rs12133115	0.83[EUR][1000 genomes]
rs12133369	0.91[EUR][1000 genomes]
rs12133849	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12134837	0.89[EUR][1000 genomes]
rs12134886	0.96[EUR][1000 genomes]
rs12135057	0.89[EUR][1000 genomes]
rs12135355	0.80[EUR][1000 genomes]
rs12135361	0.89[EUR][1000 genomes]
rs12135436	0.80[EUR][1000 genomes]
rs12135559	0.89[EUR][1000 genomes]
rs12135642	0.89[EUR][1000 genomes]
rs12135726	0.89[EUR][1000 genomes]
rs12136425	0.89[EUR][1000 genomes]
rs12138861	0.89[EUR][1000 genomes]
rs12140134	0.96[EUR][1000 genomes]
rs12140656	0.89[EUR][1000 genomes]
rs12140984	0.91[EUR][1000 genomes]
rs12141317	0.89[EUR][1000 genomes]
rs12141572	0.89[EUR][1000 genomes]
rs12142093	0.89[EUR][1000 genomes]
rs12142355	0.96[EUR][1000 genomes]
rs12142511	0.89[EUR][1000 genomes]
rs12143057	0.89[EUR][1000 genomes]
rs12143161	0.89[EUR][1000 genomes]
rs12143260	0.83[EUR][1000 genomes]
rs12143301	0.89[EUR][1000 genomes]
rs12143739	0.87[EUR][1000 genomes]
rs12143781	0.83[EUR][1000 genomes]
rs12144122	0.93[EUR][1000 genomes]
rs12144204	0.89[EUR][1000 genomes]
rs12144207	0.89[EUR][1000 genomes]
rs12144599	0.82[EUR][1000 genomes]
rs12144624	0.93[EUR][1000 genomes]
rs12144683	0.93[EUR][1000 genomes]
rs12145295	0.83[EUR][1000 genomes]
rs12145417	0.89[EUR][1000 genomes]
rs12145458	0.89[EUR][1000 genomes]
rs12145574	0.89[EUR][1000 genomes]
rs12145705	0.83[EUR][1000 genomes]
rs12146043	0.93[EUR][1000 genomes]
rs1321657	0.83[EUR][1000 genomes]
rs1496	0.89[EUR][1000 genomes]
rs16828222	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16862751	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16862919	0.87[EUR][1000 genomes]
rs16862956	0.87[EUR][1000 genomes]
rs16862968	0.87[EUR][1000 genomes]
rs17349733	0.83[EUR][1000 genomes]
rs17349740	0.83[EUR][1000 genomes]
rs17529304	0.89[EUR][1000 genomes]
rs17529791	0.89[EUR][1000 genomes]
rs17543370	0.89[EUR][1000 genomes]
rs17543611	0.89[EUR][1000 genomes]
rs17543730	0.89[EUR][1000 genomes]
rs17544586	0.93[EUR][1000 genomes]
rs17544823	0.93[EUR][1000 genomes]
rs17593862	0.81[EUR][1000 genomes]
rs17601414	0.89[EUR][1000 genomes]
rs17601582	0.89[EUR][1000 genomes]
rs17601631	0.89[EUR][1000 genomes]
rs17602051	0.89[EUR][1000 genomes]
rs17602072	0.89[EUR][1000 genomes]
rs17602701	0.89[EUR][1000 genomes]
rs17603570	0.93[EUR][1000 genomes]
rs17603666	0.93[EUR][1000 genomes]
rs2057249	0.83[EUR][1000 genomes]
rs2093050	0.91[EUR][1000 genomes]
rs2145046	0.91[EUR][1000 genomes]
rs2272919	0.89[EUR][1000 genomes]
rs2272920	0.89[EUR][1000 genomes]
rs2272921	0.88[EUR][1000 genomes]
rs2474698	0.83[EUR][1000 genomes]
rs2474704	0.87[EUR][1000 genomes]
rs2474705	0.88[EUR][1000 genomes]
rs2750018	0.91[EUR][1000 genomes]
rs2750019	0.91[EUR][1000 genomes]
rs2806384	0.91[EUR][1000 genomes]
rs2806385	0.91[EUR][1000 genomes]
rs2806387	0.91[EUR][1000 genomes]
rs2806389	0.91[EUR][1000 genomes]
rs2806390	0.91[EUR][1000 genomes]
rs2806392	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28652825	0.96[EUR][1000 genomes]
rs3766135	0.89[EUR][1000 genomes]
rs3766141	0.89[EUR][1000 genomes]
rs3766143	0.89[EUR][1000 genomes]
rs3766152	0.93[EUR][1000 genomes]
rs41272481	0.89[EUR][1000 genomes]
rs41304562	0.89[EUR][1000 genomes]
rs4385776	0.83[EUR][1000 genomes]
rs4519	0.91[EUR][1000 genomes]
rs476485	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs478116	0.91[EUR][1000 genomes]
rs483103	0.83[EUR][1000 genomes]
rs486431	0.91[EUR][1000 genomes]
rs490469	0.91[EUR][1000 genomes]
rs490776	0.83[EUR][1000 genomes]
rs495092	0.91[EUR][1000 genomes]
rs495642	0.83[EUR][1000 genomes]
rs505336	0.83[EUR][1000 genomes]
rs506196	0.83[EUR][1000 genomes]
rs510681	0.83[EUR][1000 genomes]
rs511443	0.84[EUR][1000 genomes]
rs511609	0.83[EUR][1000 genomes]
rs517649	0.91[EUR][1000 genomes]
rs518928	0.91[EUR][1000 genomes]
rs520990	0.83[EUR][1000 genomes]
rs521165	0.88[EUR][1000 genomes]
rs522017	0.91[EUR][1000 genomes]
rs536080	0.85[EUR][1000 genomes]
rs536358	0.88[EUR][1000 genomes]
rs536834	0.82[EUR][1000 genomes]
rs537976	0.85[EUR][1000 genomes]
rs541711	0.91[EUR][1000 genomes]
rs544008	0.91[EUR][1000 genomes]
rs545954	0.84[EUR][1000 genomes]
rs545963	0.88[EUR][1000 genomes]
rs549537	0.91[EUR][1000 genomes]
rs553209	0.91[EUR][1000 genomes]
rs554060	0.91[EUR][1000 genomes]
rs557475	0.83[EUR][1000 genomes]
rs558540	0.83[EUR][1000 genomes]
rs558782	0.91[EUR][1000 genomes]
rs559969	0.88[EUR][1000 genomes]
rs560414	0.91[EUR][1000 genomes]
rs562054	0.83[EUR][1000 genomes]
rs562837	0.88[EUR][1000 genomes]
rs565397	0.91[EUR][1000 genomes]
rs565626	0.93[EUR][1000 genomes]
rs571806	0.85[EUR][1000 genomes]
rs575147	0.91[EUR][1000 genomes]
rs576225	0.91[EUR][1000 genomes]
rs578916	0.88[EUR][1000 genomes]
rs57952001	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs579553	0.91[EUR][1000 genomes]
rs582900	0.91[EUR][1000 genomes]
rs583604	0.82[EUR][1000 genomes]
rs590181	0.91[EUR][1000 genomes]
rs591202	0.91[EUR][1000 genomes]
rs591559	0.91[EUR][1000 genomes]
rs593406	0.91[EUR][1000 genomes]
rs595984	0.85[EUR][1000 genomes]
rs598763	0.91[EUR][1000 genomes]
rs601355	0.91[EUR][1000 genomes]
rs602556	0.91[EUR][1000 genomes]
rs606047	0.91[EUR][1000 genomes]
rs606409	0.91[EUR][1000 genomes]
rs606689	0.80[EUR][1000 genomes]
rs606695	0.80[EUR][1000 genomes]
rs607707	0.83[EUR][1000 genomes]
rs612548	0.88[EUR][1000 genomes]
rs615485	0.91[EUR][1000 genomes]
rs615915	0.83[EUR][1000 genomes]
rs61620667	0.94[AFR][1000 genomes]
rs616789	0.83[EUR][1000 genomes]
rs618149	0.91[EUR][1000 genomes]
rs629408	0.83[EUR][1000 genomes]
rs629593	0.87[EUR][1000 genomes]
rs630179	0.83[EUR][1000 genomes]
rs638486	0.83[EUR][1000 genomes]
rs642352	0.91[EUR][1000 genomes]
rs6427231	0.82[EUR][1000 genomes]
rs644834	0.88[EUR][1000 genomes]
rs646730	0.87[EUR][1000 genomes]
rs647113	0.91[EUR][1000 genomes]
rs648502	0.88[EUR][1000 genomes]
rs654664	0.85[EUR][1000 genomes]
rs655133	0.91[EUR][1000 genomes]
rs655474	0.85[EUR][1000 genomes]
rs656334	0.91[EUR][1000 genomes]
rs656848	0.91[EUR][1000 genomes]
rs657254	0.91[EUR][1000 genomes]
rs659363	0.84[EUR][1000 genomes]
rs661516	0.80[EUR][1000 genomes]
rs664598	0.91[EUR][1000 genomes]
rs664962	0.91[EUR][1000 genomes]
rs665774	0.87[EUR][1000 genomes]
rs6672131	0.99[AFR][1000 genomes]
rs6681685	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6691861	0.99[AFR][1000 genomes]
rs6692172	0.93[AFR][1000 genomes]
rs671921	0.91[EUR][1000 genomes]
rs672843	0.91[EUR][1000 genomes]
rs673280	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs673656	0.85[EUR][1000 genomes]
rs673789	0.91[EUR][1000 genomes]
rs674896	0.88[EUR][1000 genomes]
rs675394	0.88[EUR][1000 genomes]
rs676020	0.91[EUR][1000 genomes]
rs677630	0.88[EUR][1000 genomes]
rs680269	0.83[EUR][1000 genomes]
rs685155	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs686519	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs686911	0.87[EUR][1000 genomes]
rs687195	0.83[EUR][1000 genomes]
rs74122419	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs850771	0.83[EUR][1000 genomes]
rs9426888	0.83[EUR][1000 genomes]
rs9645328	0.89[EUR][1000 genomes]
rs9645329	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12129052	METTL18	cis	Adipose Subcutaneous	GTEx
rs12129052	METTL18	cis	Stomach	GTEx
rs12129052	METTL18	cis	Esophagus Mucosa	GTEx
rs12129052	METTL18	cis	Artery Aorta	GTEx
rs12129052	METTL18	cis	lung	GTEx
rs12129052	METTL18	cis	Heart Left Ventricle	GTEx
rs12129052	METTL18	cis	Nerve Tibial	GTEx
rs12129052	METTL18	cis	Thyroid	GTEx
rs12129052	METTL18	cis	Esophagus Muscularis	GTEx
rs12129052	METTL18	cis	Muscle Skeletal	GTEx
rs12129052	C1orf156	Cis_1M	lymphoblastoid	RTeQTL
rs12129052	METTL18	cis	Artery Tibial	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169872800-169887800	Weak transcription	Primary T cells from cord blood	blood
2	chr1:169875800-169889800	Weak transcription	Fetal Brain Female	brain
3	chr1:169876200-169903600	Weak transcription	Aorta	Aorta
4	chr1:169876600-169883000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:169876800-169883400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:169877000-169884000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:169877600-169889800	Weak transcription	Lung	lung
8	chr1:169878400-169882400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:169878400-169892200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:169878400-169895200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:169878400-169946200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:169878600-169883600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:169878600-169895000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:169880200-169892800	Weak transcription	Fetal Heart	heart

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