Variant report

Variant	rs1897532
Chromosome Location	chr5:147576861-147576862
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 142 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs10041939	0.86[EUR][1000 genomes]
rs10052031	0.80[EUR][1000 genomes]
rs10055396	0.82[EUR][1000 genomes]
rs10058776	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10059441	0.84[EUR][1000 genomes]
rs10063951	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10065999	0.92[CEU][hapmap]
rs10067334	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs10068988	0.92[CEU][hapmap]
rs10074328	0.82[EUR][1000 genomes]
rs10077607	0.82[EUR][1000 genomes]
rs10079388	0.96[EUR][1000 genomes]
rs10079716	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10477363	0.83[EUR][1000 genomes]
rs10491344	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11168037	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11168038	0.97[EUR][1000 genomes]
rs11168039	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11168041	0.97[EUR][1000 genomes]
rs11743040	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11743518	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11743523	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11745313	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11748034	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12188857	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12189210	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12332436	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12332677	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12515246	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12515885	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12516461	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12519059	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12519106	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12519629	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12521387	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12522694	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12653723	0.81[EUR][1000 genomes]
rs12653724	0.81[EUR][1000 genomes]
rs12717963	0.87[EUR][1000 genomes]
rs13154742	0.82[EUR][1000 genomes]
rs13174534	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13174816	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13174845	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13175245	0.98[EUR][1000 genomes]
rs13179181	0.89[EUR][1000 genomes]
rs13185600	0.97[EUR][1000 genomes]
rs13360182	0.88[CEU][hapmap]
rs1368305	0.97[EUR][1000 genomes]
rs1368306	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs1432689	0.92[CEU][hapmap];0.97[EUR][1000 genomes]
rs1558410	0.83[EUR][1000 genomes]
rs17096690	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs17096693	0.99[EUR][1000 genomes]
rs17107871	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1812484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1897533	0.97[EUR][1000 genomes]
rs1974627	0.83[EUR][1000 genomes]
rs1974628	0.83[EUR][1000 genomes]
rs1974629	0.83[EUR][1000 genomes]
rs2017896	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2159661	0.83[EUR][1000 genomes]
rs2191680	0.93[CEU][hapmap]
rs2191681	0.83[EUR][1000 genomes]
rs2400493	0.83[EUR][1000 genomes]
rs2400494	0.83[EUR][1000 genomes]
rs2400495	0.83[EUR][1000 genomes]
rs2400496	0.83[EUR][1000 genomes]
rs2400497	0.83[EUR][1000 genomes]
rs2400498	0.83[EUR][1000 genomes]
rs28406596	0.97[EUR][1000 genomes]
rs28624399	0.97[EUR][1000 genomes]
rs28667181	0.97[EUR][1000 genomes]
rs28701955	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34211205	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34258096	0.84[EUR][1000 genomes]
rs34339574	0.83[EUR][1000 genomes]
rs34506706	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35217112	0.84[EUR][1000 genomes]
rs35491588	0.85[EUR][1000 genomes]
rs35507985	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35696310	0.82[EUR][1000 genomes]
rs36056267	0.84[EUR][1000 genomes]
rs4133459	0.97[EUR][1000 genomes]
rs4254894	0.92[CEU][hapmap]
rs4259160	0.83[EUR][1000 genomes]
rs4269285	0.92[CEU][hapmap]
rs4270684	0.83[EUR][1000 genomes]
rs4452547	0.83[EUR][1000 genomes]
rs4498243	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4499819	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4705231	0.97[EUR][1000 genomes]
rs4705232	0.97[EUR][1000 genomes]
rs4705233	0.97[EUR][1000 genomes]
rs4705234	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6580532	0.82[EUR][1000 genomes]
rs6580533	0.82[EUR][1000 genomes]
rs6580534	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6580535	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6580536	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6860003	0.82[EUR][1000 genomes]
rs6864124	0.86[EUR][1000 genomes]
rs6865006	0.97[EUR][1000 genomes]
rs6865474	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6867695	0.85[EUR][1000 genomes]
rs6868569	0.86[EUR][1000 genomes]
rs6869054	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6870548	0.84[EUR][1000 genomes]
rs6871633	0.84[EUR][1000 genomes]
rs6875563	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881658	0.92[CEU][hapmap]
rs6884944	0.82[EUR][1000 genomes]
rs6895745	0.92[CEU][hapmap]
rs6896988	0.84[EUR][1000 genomes]
rs7442844	0.97[EUR][1000 genomes]
rs7442875	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7444240	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7445428	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7445725	0.83[EUR][1000 genomes]
rs7448271	0.97[EUR][1000 genomes]
rs7449160	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs767568	0.83[EUR][1000 genomes]
rs767569	0.83[EUR][1000 genomes]
rs767570	0.83[EUR][1000 genomes]
rs7702990	0.86[EUR][1000 genomes]
rs7703690	0.84[EUR][1000 genomes]
rs7703761	0.83[EUR][1000 genomes]
rs7705007	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7716861	0.86[EUR][1000 genomes]
rs7717699	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7719535	0.84[EUR][1000 genomes]
rs7732604	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9325084	0.83[EUR][1000 genomes]
rs9325087	0.86[EUR][1000 genomes]
rs9325088	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs963016	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9885020	0.82[EUR][1000 genomes]
rs9885270	0.82[EUR][1000 genomes]
rs9885451	0.96[CEU][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][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	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	nsv980947	chr5:147571596-147583858	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv1845496	chr5:147576457-147586789	Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1897532	SPINK6	cis	Esophagus Mucosa	GTEx
rs1897532	FBXO38	cis	Whole Blood	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147572200-147582000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:147573200-147584000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:147576000-147581000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:147576200-147581400	Weak transcription	NHEK	skin
5	chr5:147576600-147582400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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