Variant report

Variant	rs3902397
Chromosome Location	chr21:29065059-29065060
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 128 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10211858	0.92[ASN][1000 genomes]
rs10211869	0.96[ASN][1000 genomes]
rs10211870	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1041802	0.96[ASN][1000 genomes]
rs11088039	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1155159	0.96[ASN][1000 genomes]
rs12152077	0.93[ASN][1000 genomes]
rs1367712	0.81[ASN][1000 genomes]
rs1367718	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1367719	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1475586	0.96[ASN][1000 genomes]
rs1557386	0.96[ASN][1000 genomes]
rs1560471	0.96[ASN][1000 genomes]
rs17646172	0.82[ASN][1000 genomes]
rs1835648	0.96[ASN][1000 genomes]
rs1835649	0.96[ASN][1000 genomes]
rs2017308	0.96[ASN][1000 genomes]
rs2831047	0.83[ASN][1000 genomes]
rs2831058	0.96[ASN][1000 genomes]
rs2831059	0.96[ASN][1000 genomes]
rs2831060	0.96[ASN][1000 genomes]
rs2831061	0.96[ASN][1000 genomes]
rs2831062	0.96[ASN][1000 genomes]
rs2831063	0.96[ASN][1000 genomes]
rs2831064	0.96[ASN][1000 genomes]
rs2831066	0.96[ASN][1000 genomes]
rs2831067	0.96[ASN][1000 genomes]
rs2831068	0.96[ASN][1000 genomes]
rs2831070	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2831071	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2831072	0.95[ASN][1000 genomes]
rs2831073	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2831074	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2831075	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2831076	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2831077	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2831078	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2831079	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2831080	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2831081	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2831082	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2831083	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2831084	0.96[ASN][1000 genomes]
rs2831085	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2831087	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2831088	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2831089	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2831090	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2831091	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2831092	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2831094	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2831096	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2831097	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2831098	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2831099	0.82[ASN][1000 genomes]
rs2831102	0.82[ASN][1000 genomes]
rs2831103	0.82[ASN][1000 genomes]
rs28394464	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28470885	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28576337	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28786796	0.92[ASN][1000 genomes]
rs2898115	0.96[ASN][1000 genomes]
rs3906629	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3910128	0.97[ASN][1000 genomes]
rs3910129	0.97[ASN][1000 genomes]
rs3910130	0.97[ASN][1000 genomes]
rs4113960	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4113961	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4113967	0.89[ASN][1000 genomes]
rs4113968	0.87[ASN][1000 genomes]
rs4438569	0.93[ASN][1000 genomes]
rs5005234	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5005235	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5005236	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5005237	0.95[ASN][1000 genomes]
rs715241	0.96[ASN][1000 genomes]
rs715242	0.96[ASN][1000 genomes]
rs7281308	0.81[ASN][1000 genomes]
rs73183739	0.95[ASN][1000 genomes]
rs7510446	0.95[ASN][1000 genomes]
rs914133	0.96[ASN][1000 genomes]
rs914134	0.96[ASN][1000 genomes]
rs9653692	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9653693	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9974135	0.93[ASN][1000 genomes]
rs9974297	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9974860	0.93[ASN][1000 genomes]
rs9975519	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9975804	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9976066	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9976248	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9977067	0.93[ASN][1000 genomes]
rs9977138	0.83[ASN][1000 genomes]
rs9977323	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9977452	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9977509	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9977527	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9979154	0.96[ASN][1000 genomes]
rs9979177	0.93[ASN][1000 genomes]
rs9979321	0.96[ASN][1000 genomes]
rs9979569	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9979996	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9980014	0.93[ASN][1000 genomes]
rs9981215	0.93[ASN][1000 genomes]
rs9981239	0.81[ASN][1000 genomes]
rs9981404	0.95[ASN][1000 genomes]
rs9981772	0.96[ASN][1000 genomes]
rs9982537	0.96[ASN][1000 genomes]
rs9982546	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9982677	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9983211	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9983340	0.96[ASN][1000 genomes]
rs9983405	0.95[ASN][1000 genomes]
rs9983418	0.96[ASN][1000 genomes]
rs9983492	0.96[ASN][1000 genomes]
rs9983636	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9983784	0.96[ASN][1000 genomes]
rs9983804	0.96[ASN][1000 genomes]
rs9983943	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9983947	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9983950	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9984837	0.86[ASN][1000 genomes]
rs9985086	0.80[EUR][1000 genomes];0.96[ASN][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	nsv459229	chr21:28543456-29482488	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv587342	chr21:28543456-29482488	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1059423	chr21:28957144-29306656	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv913670	chr21:29022265-29525767	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1059134	chr21:29061408-29188185	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:29063400-29065400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr21:29063800-29065400	Weak transcription	HSMM	muscle
3	chr21:29064000-29066400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr21:29064800-29065400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr21:29064800-29065600	Enhancers	HMEC	breast
6	chr21:29064800-29067400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr21:29065000-29065800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr21:29065000-29065800	Enhancers	Osteobl	bone

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