Variant report

Variant	rs1973400
Chromosome Location	chr3:23310881-23310882
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1013460	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1027379	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11129113	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11129116	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11708117	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11708176	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11717397	0.90[ASN][1000 genomes]
rs11720461	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11920019	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12330262	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12330479	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12493361	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12496983	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12497974	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12629848	0.92[ASN][1000 genomes]
rs12715047	0.84[ASN][1000 genomes]
rs13074192	0.87[ASN][1000 genomes]
rs13080261	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13080401	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13081371	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13321359	0.82[ASN][1000 genomes]
rs13326048	0.84[ASN][1000 genomes]
rs1495131	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1532355	0.95[ASN][1000 genomes]
rs1552930	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17012812	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17012869	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1874235	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2055154	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2172828	0.90[ASN][1000 genomes]
rs2359759	0.85[ASN][1000 genomes]
rs34919006	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4241511	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4241512	0.86[ASN][1000 genomes]
rs4488778	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4858062	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4858064	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4858071	0.87[ASN][1000 genomes]
rs4858072	0.87[ASN][1000 genomes]
rs4858077	0.82[ASN][1000 genomes]
rs4858483	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4858484	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4858491	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4858492	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858496	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858497	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4858500	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4858501	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4858502	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4858504	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4858506	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4858508	0.92[ASN][1000 genomes]
rs4858509	0.85[ASN][1000 genomes]
rs4858511	0.87[ASN][1000 genomes]
rs59429714	0.93[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6550746	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6550748	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6550755	0.83[ASN][1000 genomes]
rs6550756	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6769173	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6784195	0.85[ASN][1000 genomes]
rs6784771	0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6795492	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6796840	0.83[ASN][1000 genomes]
rs6804123	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6805889	0.86[ASN][1000 genomes]
rs716457	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7429470	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7617072	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7622784	0.90[ASN][1000 genomes]
rs7631334	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs778460	0.80[AMR][1000 genomes]
rs778485	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs778487	0.82[AMR][1000 genomes]
rs778488	0.81[ASN][1000 genomes]
rs778494	0.81[AMR][1000 genomes]
rs9310715	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9809176	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9816895	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9821101	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9822422	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9825778	0.87[ASN][1000 genomes]
rs9826089	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9826647	0.85[ASN][1000 genomes]
rs9826877	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9836787	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9839738	0.87[ASN][1000 genomes]
rs9840820	0.83[ASN][1000 genomes]
rs9841123	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9841944	0.90[ASN][1000 genomes]
rs9846398	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9847027	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9847958	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9848077	0.82[ASN][1000 genomes]
rs9849176	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849424	0.85[ASN][1000 genomes]
rs9853489	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9854148	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9854590	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9859515	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9859651	0.85[ASN][1000 genomes]
rs9861803	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9864908	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9865602	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9873317	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9874082	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9874519	0.90[ASN][1000 genomes]
rs9874822	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][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	nsv1014701	chr3:23257658-23416094	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv589947	chr3:23277838-23403943	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv589948	chr3:23287141-23390221	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23295200-23321800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:23298800-23311000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:23298800-23336600	Weak transcription	Thymus	Thymus
4	chr3:23299000-23314200	Weak transcription	Primary T cells from cord blood	blood
5	chr3:23302400-23312800	Weak transcription	Lung	lung
6	chr3:23302400-23321000	Weak transcription	Pancreas	Pancrea
7	chr3:23305200-23311000	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:23305600-23318400	Weak transcription	Brain Substantia Nigra	brain
9	chr3:23306600-23311600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:23306800-23312800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:23306800-23314200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:23307000-23311000	Weak transcription	Primary B cells from peripheral blood	blood
13	chr3:23307200-23313200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:23307200-23313400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:23307200-23314400	Weak transcription	HSMMtube	muscle
16	chr3:23307200-23316000	Weak transcription	Primary B cells from cord blood	blood
17	chr3:23310800-23311000	Enhancers	Spleen	Spleen
18	chr3:23310800-23311400	Enhancers	Skeletal Muscle Male	skeletal muscle

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