Variant report

Variant	rs9728169
Chromosome Location	chr1:47524264-47524265
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs1021827	0.82[GIH][hapmap];0.87[MEX][hapmap];0.89[YRI][hapmap]
rs10890445	0.82[GIH][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.89[YRI][hapmap]
rs10890446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890449	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10890452	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10890453	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10890454	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10890455	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10890457	0.89[ASW][hapmap];0.83[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap]
rs10890460	0.89[ASW][hapmap];0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10890462	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10890464	0.89[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10890465	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10890466	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10890467	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1110425	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1117514	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211421	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211422	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs11211423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211435	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211439	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11211442	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11211444	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11211446	0.83[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs11211450	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11211451	0.89[ASW][hapmap];0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap]
rs11211454	0.80[EUR][1000 genomes]
rs11211456	0.82[AMR][1000 genomes]
rs11211457	0.83[CEU][hapmap];0.86[YRI][hapmap];0.81[EUR][1000 genomes]
rs12022635	1.00[ASW][hapmap];0.95[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12037014	0.89[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12042073	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12046348	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12124648	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12404496	0.87[ASN][1000 genomes]
rs12564635	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12567857	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12568064	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12732488	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12734327	0.89[ASW][hapmap];0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12736235	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393659	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393667	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1502908	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1553391	0.86[AMR][1000 genomes]
rs1847222	0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.82[EUR][1000 genomes]
rs1847223	0.82[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1847224	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1967756	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1967757	0.89[ASW][hapmap];0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2016160	0.83[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs2055500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2134471	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2202219	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405588	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494248	0.81[TSI][hapmap]
rs28462300	0.82[AMR][1000 genomes]
rs3117713	0.81[AMR][1000 genomes]
rs35900382	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3850876	0.80[EUR][1000 genomes]
rs4314923	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4375314	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4448558	1.00[JPT][hapmap];0.89[YRI][hapmap]
rs4492665	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4598535	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4926773	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4926785	0.89[ASW][hapmap];0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4926786	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4926787	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4926788	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4926789	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4926791	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4926792	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4926793	0.89[ASW][hapmap];0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4926797	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4926804	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4926805	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4926806	0.83[AMR][1000 genomes]
rs4926807	0.83[AMR][1000 genomes]
rs4926808	0.83[AMR][1000 genomes]
rs4926809	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4926826	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4926869	0.81[AMR][1000 genomes]
rs6588388	0.81[AMR][1000 genomes]
rs6664392	0.89[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6664496	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6669621	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs66753730	0.86[AFR][1000 genomes]
rs6675902	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6683137	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6690005	0.89[ASW][hapmap];0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6693145	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6701611	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7512729	0.82[AMR][1000 genomes]
rs7519903	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7526674	0.82[EUR][1000 genomes]
rs7540264	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7545399	0.89[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes]
rs7547893	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9326151	0.82[GIH][hapmap];0.87[MEX][hapmap];0.89[YRI][hapmap]
rs9326152	0.82[GIH][hapmap];0.82[MEX][hapmap];0.89[YRI][hapmap]
rs9326153	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9633421	0.81[EUR][1000 genomes]
rs9659815	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9699932	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9701154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9701868	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9701886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9701899	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9729662	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9793202	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9793471	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9793711	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9793716	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009338	chr1:47358532-47555253	Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2763300	chr1:47358532-47628774	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv916813	chr1:47435635-47666179	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv871717	chr1:47449486-47524264	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv461428	chr1:47487585-47524264	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv546167	chr1:47487585-47524264	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9728169	AKR1A1	cis	parietal	SCAN
rs9728169	SPATA6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47524000-47524400	ZNF genes & repeats	Aorta	Aorta
2	chr1:47524200-47524400	Bivalent/Poised TSS	Primary T helper cells fromperipheralblood	blood

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