Variant report

Variant	rs10890459
Chromosome Location	chr1:47573980-47573981
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1021827	0.89[MKK][hapmap]
rs10890445	0.91[MKK][hapmap]
rs10890446	0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs10890447	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs10890457	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap]
rs10890458	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890460	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10890462	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10890464	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes]
rs10890465	0.82[AMR][1000 genomes]
rs10890466	0.82[AMR][1000 genomes]
rs10890467	0.82[AMR][1000 genomes]
rs1110425	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11211422	0.89[ASW][hapmap];0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.97[MKK][hapmap];0.89[YRI][hapmap]
rs11211423	0.83[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs11211439	0.94[ASW][hapmap];0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap]
rs11211446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11211450	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11211451	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs11211454	0.80[AMR][1000 genomes]
rs11211457	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs12022635	0.89[ASW][hapmap];0.83[CHD][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.85[YRI][hapmap]
rs12037014	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12042073	0.82[AMR][1000 genomes]
rs12046348	0.82[AMR][1000 genomes]
rs12124648	0.82[AMR][1000 genomes]
rs12564635	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap]
rs12734327	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12736235	0.94[ASW][hapmap];0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap]
rs1393667	0.94[ASW][hapmap];0.83[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap]
rs1502908	0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs1847222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes]
rs1847223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1847224	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1967756	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1967757	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2016160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2055500	0.83[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs2134471	0.83[CEU][hapmap]
rs2405580	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs2742079	0.87[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs2798352	0.87[CEU][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs28462300	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs28723590	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3117713	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4314923	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4448558	1.00[JPT][hapmap];0.93[YRI][hapmap]
rs4926785	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4926786	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4926787	0.84[AMR][1000 genomes]
rs4926788	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4926789	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4926791	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4926792	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4926793	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4926797	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4926804	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4926805	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4926806	0.83[AMR][1000 genomes]
rs4926807	0.83[AMR][1000 genomes]
rs4926808	0.83[AMR][1000 genomes]
rs4926809	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4926826	0.86[AMR][1000 genomes]
rs4926869	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6588388	0.81[AMR][1000 genomes]
rs6588389	0.80[AMR][1000 genomes]
rs6664392	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes]
rs6664496	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes]
rs6675902	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6690005	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6693145	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6701611	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6704068	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7512729	0.82[AMR][1000 genomes]
rs7519903	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7522639	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7526674	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7540264	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7545399	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes]
rs7547893	0.81[AMR][1000 genomes]
rs9326151	0.89[MKK][hapmap]
rs9326152	0.89[MKK][hapmap]
rs9633421	0.81[AMR][1000 genomes]
rs9701154	0.83[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs9793202	0.89[ASW][hapmap];0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap]
rs9793471	0.87[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs9793716	0.83[CEU][hapmap];0.81[TSI][hapmap]

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	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
2	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
3	nsv870705	chr1:47533705-47620126	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871010	chr1:47533705-47637999	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv870899	chr1:47548974-47637999	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv13964	chr1:47565590-47574182	Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47572200-47574400	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr1:47572200-47574800	Enhancers	HMEC	breast
3	chr1:47573200-47574800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:47573200-47578000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:47573600-47574000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:47573600-47574400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr1:47573600-47574400	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr1:47573600-47574600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:47573600-47575600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:47573600-47575600	Enhancers	Hela-S3	cervix
11	chr1:47573600-47575600	Enhancers	NHEK	skin
12	chr1:47573600-47577200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:47573600-47578600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:47573800-47574200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:47573800-47574200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:47573800-47574600	Enhancers	HUVEC	blood vessel

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