Variant report

Variant	rs4259160
Chromosome Location	chr5:147557190-147557191
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 162 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
rs10041939	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10043288	0.88[AMR][1000 genomes]
rs10052031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10055396	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10058776	0.82[EUR][1000 genomes]
rs10059441	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10061827	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10063951	0.81[EUR][1000 genomes]
rs10065999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10067334	0.96[CEU][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs10068904	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10068913	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10068916	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10068922	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10068988	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10070470	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10074328	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10075227	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10077607	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10079388	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10079716	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs10477363	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10491344	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11168037	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11168038	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11168039	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11168041	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11743040	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11743518	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11743523	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11745313	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11748034	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12188857	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12189210	0.90[EUR][1000 genomes]
rs12332436	0.89[CEU][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs12332677	0.89[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs12515246	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12515885	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12516461	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12519059	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12519106	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12519629	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12521387	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12522694	0.89[EUR][1000 genomes]
rs12653723	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12653724	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12717963	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13154742	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13174534	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13174816	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13174845	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13175245	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13179181	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13185600	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13360182	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1368305	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1368306	0.89[CEU][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1432689	0.84[CEU][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1558410	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17096690	0.92[CEU][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17096693	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17107871	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1812484	0.81[EUR][1000 genomes]
rs1897532	0.83[EUR][1000 genomes]
rs1897533	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1974627	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1974628	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1974629	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017896	0.83[EUR][1000 genomes]
rs2159661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2191680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2191681	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2400488	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2400491	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2400492	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2400493	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400496	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400497	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400498	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28406596	0.82[EUR][1000 genomes]
rs28624399	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28667181	0.82[EUR][1000 genomes]
rs28701955	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34211205	0.83[EUR][1000 genomes]
rs34258096	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34339574	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34506706	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35217112	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35491588	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35507985	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35696310	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36056267	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4133459	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4254894	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4269285	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4270684	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4452547	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4498243	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4499819	0.90[EUR][1000 genomes]
rs4705230	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4705231	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4705232	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4705233	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4705234	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6580532	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6580533	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6580534	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6580535	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6580536	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6860003	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6864124	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6865006	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6865474	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6867695	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6868569	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6869054	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6870548	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6871633	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6872890	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6875563	0.82[EUR][1000 genomes]
rs6881658	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs6884944	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6894796	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6895745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs6896988	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7442844	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7442875	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7444240	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7445428	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7445725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7448271	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7449160	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs767568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs767569	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs767570	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7702990	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7703690	0.83[EUR][1000 genomes]
rs7703761	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7705007	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7716861	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7717500	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7717699	0.84[EUR][1000 genomes]
rs7719535	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7732604	0.82[EUR][1000 genomes]
rs9285669	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9325077	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9325078	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9325084	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9325087	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9325088	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs963016	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9885020	0.90[EUR][1000 genomes]
rs9885270	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9885333	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9885451	0.96[CEU][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883015	chr5:147404281-147751035	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv830515	chr5:147460852-147602247	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv1846741	chr5:147553186-147557190	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
4	esv1847617	chr5:147553186-147557190	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
5	esv1843289	chr5:147554337-147576457	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4259160	SPINK6	cis	Esophagus Mucosa	GTEx
rs4259160	SPINK1	cis	cerebellum	SCAN
rs4259160	FFAR2	trans	cerebellum	SCAN
rs4259160	TFF3	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147552200-147559800	Weak transcription	Stomach Mucosa	stomach
2	chr5:147556400-147557200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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