Variant report

Variant	rs7542775
Chromosome Location	chr1:174530902-174530903
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174527785..174529980-chr1:174530540..174532967,2	MCF-7	breast:

Extended variants
information (count: 159 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs10489264	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10798311	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10798319	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10912774	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10912782	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10912799	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10912800	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10912817	0.97[ASN][1000 genomes]
rs10912820	0.91[EUR][1000 genomes]
rs10912821	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10912822	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10912823	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912828	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10912829	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11487399	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11487400	0.87[ASN][1000 genomes]
rs11487401	0.87[ASN][1000 genomes]
rs11802092	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11805578	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11806996	0.81[ASN][1000 genomes]
rs12062016	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12062170	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12062483	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12063545	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12064403	0.89[ASN][1000 genomes]
rs12064743	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12064749	0.87[ASN][1000 genomes]
rs12065825	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12067463	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12071794	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12077529	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12079118	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12079757	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12079879	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12080535	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12082012	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12082139	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12083628	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12085652	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12086693	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12092768	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1474575	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs149099	0.92[ASN][1000 genomes]
rs1618408	0.88[EUR][1000 genomes]
rs162815	0.86[EUR][1000 genomes]
rs1653636	0.82[EUR][1000 genomes]
rs16846938	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs16847335	0.92[ASN][1000 genomes]
rs16847337	0.92[ASN][1000 genomes]
rs1754360	0.86[EUR][1000 genomes]
rs17842156	0.92[ASN][1000 genomes]
rs17842157	0.92[ASN][1000 genomes]
rs1793307	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1793310	0.88[EUR][1000 genomes]
rs193082	0.82[ASN][1000 genomes]
rs2012558	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2060158	0.92[ASN][1000 genomes]
rs2092084	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2142632	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2146564	0.92[ASN][1000 genomes]
rs2760058	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2771401	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2861003	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2861005	0.92[ASN][1000 genomes]
rs2861006	0.92[ASN][1000 genomes]
rs2901818	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3117843	0.90[ASN][1000 genomes]
rs332763	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs332764	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs332767	0.92[ASN][1000 genomes]
rs332768	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs332772	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs332779	0.92[ASN][1000 genomes]
rs332781	0.87[ASN][1000 genomes]
rs332782	0.87[ASN][1000 genomes]
rs332784	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs332786	0.92[ASN][1000 genomes]
rs332793	0.82[ASN][1000 genomes]
rs332797	0.82[ASN][1000 genomes]
rs332798	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs332806	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs333422	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs333423	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs333437	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs333438	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs333452	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs333453	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs333454	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs333471	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34409674	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3862941	0.92[ASN][1000 genomes]
rs3920486	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs395109	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs398350	0.92[ASN][1000 genomes]
rs399530	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs411665	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4451598	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4562683	0.97[ASN][1000 genomes]
rs458242	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs459078	0.86[EUR][1000 genomes]
rs4615901	0.97[ASN][1000 genomes]
rs464540	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4651103	0.97[ASN][1000 genomes]
rs4651114	0.92[ASN][1000 genomes]
rs4652500	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4652652	0.97[ASN][1000 genomes]
rs4652669	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs467437	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs5015737	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55643907	0.97[ASN][1000 genomes]
rs55667039	0.92[ASN][1000 genomes]
rs55688014	0.92[ASN][1000 genomes]
rs55945681	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs56213002	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56260545	0.97[ASN][1000 genomes]
rs56292878	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61624206	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658315	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6667107	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6668096	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6675515	0.89[ASN][1000 genomes]
rs6677874	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681970	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6689153	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6691118	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692173	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72713601	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72715240	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72715245	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72715253	0.97[ASN][1000 genomes]
rs72715255	0.97[ASN][1000 genomes]
rs72715259	0.97[ASN][1000 genomes]
rs72715260	0.97[ASN][1000 genomes]
rs72715262	0.97[ASN][1000 genomes]
rs72715273	0.92[ASN][1000 genomes]
rs7414200	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7516353	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7522253	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7530265	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535845	0.81[EUR][1000 genomes]
rs7536102	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7536987	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7554728	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7554740	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9729907	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9730220	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010069	chr1:174215293-174539512	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	nsv1007667	chr1:174438778-174556953	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1009056	chr1:174457532-174549665	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv999295	chr1:174457532-174596961	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	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
11	esv2757762	chr1:174469281-174569776	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv2758979	chr1:174469281-174569776	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
13	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7542775	RABGAP1L	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174514800-174539400	Weak transcription	Ovary	ovary
2	chr1:174529800-174538200	Weak transcription	Primary B cells from peripheral blood	blood

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