Variant report

Variant	rs2420170
Chromosome Location	chr7:65656053-65656054
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10247526	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10807699	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10807701	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10807702	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10950032	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12530490	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12667373	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13308751	0.80[AMR][1000 genomes]
rs1392104	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1499613	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1499614	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1532573	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1546059	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1553174	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs160637	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs160638	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs160639	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs160656	0.81[AMR][1000 genomes]
rs160657	0.81[AMR][1000 genomes]
rs182600	0.82[AMR][1000 genomes]
rs186378	0.82[AMR][1000 genomes]
rs1873494	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1979823	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2243480	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2257790	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2420171	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2420172	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2460422	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2460425	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2460426	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2460431	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2465120	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs313819	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs313820	0.82[AMR][1000 genomes]
rs313822	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs313824	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs313831	0.81[AMR][1000 genomes]
rs316304	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs316307	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs316313	0.82[AMR][1000 genomes]
rs316314	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs316317	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs316318	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs316321	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs316322	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs316325	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs316326	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs316327	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs316329	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs316331	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs316332	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs316333	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs316334	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34032527	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs36127118	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs383402	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs387676	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4145008	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4149468	0.84[EUR][1000 genomes]
rs419603	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs422164	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4236207	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs431076	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4481472	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4718309	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4718315	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4718316	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4718317	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4718333	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6460274	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6460277	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958289	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6958420	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6959002	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6964245	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6964530	0.82[AMR][1000 genomes]
rs6966322	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6974723	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73136349	0.80[EUR][1000 genomes]
rs7778911	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs778679	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs778683	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs778687	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7787230	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs778729	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs778732	0.80[EUR][1000 genomes]
rs778733	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7792391	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7804223	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs780453	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7808834	0.87[AMR][1000 genomes]
rs958550	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9769882	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
3	nsv1021186	chr7:65492601-65663438	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2420170	ASL	cis	multi-tissue	Pritchard
rs2420170	RP4-756H11.3	cis	lung	GTEx
rs2420170	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL
rs2420170	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs2420170	VKORC1L1	cis	Whole Blood	GTEx
rs2420170	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2420170	GUSB	cis	Whole Blood	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65652400-65656200	Enhancers	Liver	Liver
2	chr7:65652800-65660600	Weak transcription	Spleen	Spleen
3	chr7:65654800-65656200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr7:65655800-65657800	Weak transcription	HepG2	liver

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