Variant report

Variant	rs12079757
Chromosome Location	chr1:174540722-174540723
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 165 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:153)

rs_ID	r²[population]
rs1013769	0.81[EUR][1000 genomes]
rs10489260	0.81[EUR][1000 genomes]
rs10489264	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10494492	0.83[ASN][1000 genomes]
rs10912791	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10912795	0.84[EUR][1000 genomes]
rs10912806	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10912817	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912821	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912822	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912823	0.90[ASN][1000 genomes]
rs10912828	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912829	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11484645	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11802092	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11805578	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11807229	0.82[EUR][1000 genomes]
rs11809482	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12062016	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12063545	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12064403	0.85[ASN][1000 genomes]
rs12064749	0.82[ASN][1000 genomes]
rs12065454	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12065825	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12067463	0.90[ASN][1000 genomes]
rs12069134	0.80[EUR][1000 genomes]
rs12076548	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12078960	0.80[EUR][1000 genomes]
rs12079118	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12079334	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12079879	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12080535	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12081012	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12081046	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12082012	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12082139	0.90[ASN][1000 genomes]
rs12083628	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12083972	0.81[EUR][1000 genomes]
rs12084948	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12085652	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12093966	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12095679	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12097931	0.80[EUR][1000 genomes]
rs1474575	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs149099	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16847012	0.80[EUR][1000 genomes]
rs16847335	0.87[ASN][1000 genomes]
rs16847337	0.87[ASN][1000 genomes]
rs17842156	0.87[ASN][1000 genomes]
rs17842157	0.87[ASN][1000 genomes]
rs2060158	0.87[ASN][1000 genomes]
rs2072759	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2092084	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2142632	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2146564	0.87[ASN][1000 genomes]
rs2281009	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2281010	0.84[EUR][1000 genomes]
rs2281011	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2760058	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2771401	0.87[ASN][1000 genomes]
rs2861003	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2861005	0.87[ASN][1000 genomes]
rs2861006	0.87[ASN][1000 genomes]
rs2901820	0.83[EUR][1000 genomes]
rs3117843	0.85[ASN][1000 genomes]
rs332763	0.85[ASN][1000 genomes]
rs332764	0.85[ASN][1000 genomes]
rs332767	0.87[ASN][1000 genomes]
rs332768	0.87[ASN][1000 genomes]
rs332772	0.85[ASN][1000 genomes]
rs332779	0.87[ASN][1000 genomes]
rs332781	0.82[ASN][1000 genomes]
rs332782	0.82[ASN][1000 genomes]
rs332786	0.87[ASN][1000 genomes]
rs332806	0.87[ASN][1000 genomes]
rs333422	0.87[ASN][1000 genomes]
rs333423	0.85[ASN][1000 genomes]
rs333437	0.85[ASN][1000 genomes]
rs333438	0.87[ASN][1000 genomes]
rs333452	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs333454	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs333471	0.85[ASN][1000 genomes]
rs34409674	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3862941	0.87[ASN][1000 genomes]
rs3920486	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs395109	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs398350	0.87[ASN][1000 genomes]
rs399530	0.87[ASN][1000 genomes]
rs411665	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41266050	0.84[EUR][1000 genomes]
rs4451598	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4562683	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs458242	0.87[ASN][1000 genomes]
rs4615901	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs464540	0.87[ASN][1000 genomes]
rs4651103	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4651114	0.87[ASN][1000 genomes]
rs4652494	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4652511	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4652512	0.84[EUR][1000 genomes]
rs4652513	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4652652	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4652669	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs467437	0.87[ASN][1000 genomes]
rs55643907	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55667039	0.87[ASN][1000 genomes]
rs55688014	0.87[ASN][1000 genomes]
rs55748748	0.84[EUR][1000 genomes]
rs55945681	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56200626	0.82[EUR][1000 genomes]
rs56260545	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56292878	0.84[ASN][1000 genomes]
rs57512497	0.82[EUR][1000 genomes]
rs61624206	0.90[ASN][1000 genomes]
rs6663959	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6665535	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6667107	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6675515	0.85[ASN][1000 genomes]
rs6677262	0.80[EUR][1000 genomes]
rs6677874	0.90[ASN][1000 genomes]
rs6682070	0.82[EUR][1000 genomes]
rs6682997	0.82[EUR][1000 genomes]
rs6689153	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6689589	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6691118	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6696945	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6701619	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72713583	0.80[EUR][1000 genomes]
rs72713584	0.80[EUR][1000 genomes]
rs72713591	0.80[EUR][1000 genomes]
rs72713602	0.81[EUR][1000 genomes]
rs72715204	0.81[EUR][1000 genomes]
rs72715216	0.82[EUR][1000 genomes]
rs72715218	0.84[EUR][1000 genomes]
rs72715224	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72715226	0.84[EUR][1000 genomes]
rs72715237	0.82[EUR][1000 genomes]
rs72715240	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72715245	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72715253	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72715255	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72715259	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72715260	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72715262	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72715273	0.87[ASN][1000 genomes]
rs74126805	0.80[EUR][1000 genomes]
rs7414200	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7516353	0.87[ASN][1000 genomes]
rs7530265	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7537823	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7542775	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7550472	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs909533	0.84[AMR][1000 genomes];0.84[EUR][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	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1014753	chr1:174271770-174694838	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv872555	chr1:174343705-174565720	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv1007667	chr1:174438778-174556953	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1009056	chr1:174457532-174549665	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv999295	chr1:174457532-174596961	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv534381	chr1:174468168-174656796	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv2757762	chr1:174469281-174569776	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv2758979	chr1:174469281-174569776	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv548196	chr1:174525135-174559121	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12079757	RABGAP1L	cis	Esophagus Muscularis	GTEx
rs12079757	RP11-160H22.5	cis	Thyroid	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174533200-174545400	Weak transcription	Primary B cells from cord blood	blood
2	chr1:174538000-174542200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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