Variant report

Variant	rs2173460
Chromosome Location	chr3:23572606-23572607
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs11129119	0.88[CHB][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs11708160	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11711072	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs11715841	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11718082	0.95[ASN][1000 genomes]
rs11916411	1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11918529	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs12386394	0.83[EUR][1000 genomes]
rs12715048	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs13064035	0.96[ASN][1000 genomes]
rs13087861	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs13326048	0.91[JPT][hapmap]
rs1353322	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs1498809	1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1498811	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs1692612	0.91[ASN][1000 genomes]
rs1692620	0.90[ASN][1000 genomes]
rs1692650	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs1695200	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs17194786	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2036226	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2055310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2133331	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2359759	0.90[JPT][hapmap]
rs2359763	0.80[JPT][hapmap]
rs3104244	0.86[ASN][1000 genomes]
rs3111311	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34080387	0.92[ASN][1000 genomes]
rs3817002	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4383458	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4456808	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4484143	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4513393	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4635650	0.93[ASN][1000 genomes]
rs4858069	0.89[CEU][hapmap]
rs4858074	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs4858505	0.86[CEU][hapmap]
rs4858506	0.91[JPT][hapmap]
rs4858509	0.89[EUR][1000 genomes]
rs55797660	0.83[EUR][1000 genomes]
rs57137870	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58748418	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60430884	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60632986	0.83[EUR][1000 genomes]
rs62256993	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62256994	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6550755	0.82[CEU][hapmap]
rs6550766	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6550767	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6763329	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6763535	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6767599	0.94[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs6770079	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6770091	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs6775232	0.96[ASN][1000 genomes]
rs6776424	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs6780723	0.94[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6780787	0.94[CHB][hapmap];0.90[ASN][1000 genomes]
rs6784195	0.91[JPT][hapmap];0.84[YRI][hapmap]
rs6788167	0.80[ASN][1000 genomes]
rs6795470	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6795968	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs6797907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6798153	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6798328	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6805889	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs6808513	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs6810100	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs704533	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs716456	0.89[CEU][hapmap]
rs73043614	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7612666	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7613091	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7614146	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7631334	0.90[JPT][hapmap]
rs7634117	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7636826	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7640308	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7644666	0.95[ASN][1000 genomes]
rs7645209	0.94[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs7648443	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7651893	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs778468	0.91[JPT][hapmap]
rs778475	0.91[ASN][1000 genomes]
rs778476	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs778477	0.86[EUR][1000 genomes]
rs778480	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs778482	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs778494	0.91[JPT][hapmap]
rs778496	0.89[ASN][1000 genomes]
rs778499	0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs778500	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs778501	0.94[CHB][hapmap];0.90[ASN][1000 genomes]
rs778503	0.88[ASN][1000 genomes]
rs778510	0.94[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs778514	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs778521	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs778523	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs778526	0.91[ASN][1000 genomes]
rs952134	0.85[CEU][hapmap]
rs9815921	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9821419	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs9824359	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9825778	0.95[JPT][hapmap]
rs9830388	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9830392	0.87[EUR][1000 genomes]
rs9830742	0.92[ASN][1000 genomes]
rs9836574	0.82[CEU][hapmap]
rs9839738	1.00[CEU][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs9856169	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs9859651	0.90[JPT][hapmap]
rs9873317	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23550800-23598600	Weak transcription	HSMMtube	muscle
2	chr3:23553000-23589600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:23567400-23589800	Weak transcription	Psoas Muscle	Psoas
4	chr3:23569400-23578600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:23570400-23575800	Weak transcription	Brain Anterior Caudate	brain
6	chr3:23570400-23578200	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:23570600-23575600	Weak transcription	Fetal Heart	heart
8	chr3:23570600-23584400	Weak transcription	Primary T cells from cord blood	blood
9	chr3:23571200-23591600	Weak transcription	GM12878-XiMat	blood
10	chr3:23571400-23598800	Weak transcription	Adipose Nuclei	Adipose
11	chr3:23572200-23572800	Enhancers	Primary B cells from peripheral blood	blood
12	chr3:23572400-23578600	Weak transcription	Brain Substantia Nigra	brain
13	chr3:23572600-23572800	Enhancers	Primary B cells from cord blood	blood

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