Variant report

Variant	rs12657948
Chromosome Location	chr5:52835873-52835874
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10065003	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10078892	0.93[ASN][1000 genomes]
rs10471866	0.83[ASN][1000 genomes]
rs10940322	0.86[ASN][1000 genomes]
rs10940323	0.89[ASN][1000 genomes]
rs12514280	0.92[CHB][hapmap];0.85[ASN][1000 genomes]
rs13177321	0.96[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs13179304	0.83[ASN][1000 genomes]
rs1490769	0.83[CHB][hapmap]
rs1532162	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs16881474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1844697	0.92[CHB][hapmap];0.95[JPT][hapmap]
rs1873426	0.87[JPT][hapmap]
rs187658	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs189849	0.92[CHB][hapmap];0.95[JPT][hapmap]
rs2124950	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs256081	0.92[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs256082	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs256086	0.80[ASN][1000 genomes]
rs256093	0.92[CHB][hapmap];0.95[JPT][hapmap]
rs256094	0.83[CHB][hapmap]
rs256098	0.92[CHB][hapmap];0.95[JPT][hapmap]
rs256109	0.83[ASN][1000 genomes]
rs256111	0.92[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs256118	0.96[CHB][hapmap];0.95[JPT][hapmap]
rs2607478	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2607485	0.92[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2607506	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2607508	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2636993	0.83[CHB][hapmap]
rs2637002	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2637003	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2637029	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs31308	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs34071992	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs365358	0.92[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs365578	0.83[CHB][hapmap]
rs366313	0.92[CHB][hapmap];0.95[JPT][hapmap]
rs368461	0.92[CHB][hapmap];0.95[JPT][hapmap]
rs372215	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs377077	0.92[CHB][hapmap];0.95[JPT][hapmap]
rs381575	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs392169	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs404838	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs412559	0.84[CHB][hapmap]
rs4147732	0.92[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4147734	0.92[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs417550	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs425085	0.83[ASN][1000 genomes]
rs425880	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs432020	0.92[CHB][hapmap];0.95[JPT][hapmap]
rs444848	0.83[ASN][1000 genomes]
rs445347	0.92[CHB][hapmap];0.95[JPT][hapmap]
rs451881	0.92[CHB][hapmap];0.95[JPT][hapmap]
rs454735	0.80[ASN][1000 genomes]
rs4865547	0.89[ASN][1000 genomes]
rs4865548	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs524289	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs535277	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs58889983	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7711180	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7717681	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7736747	0.89[ASN][1000 genomes]
rs786334	0.92[CHB][hapmap];0.95[JPT][hapmap]
rs889290	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs918625	0.92[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs923610	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9292024	0.83[CHB][hapmap]
rs9790964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9791019	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9791152	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv880868	chr5:52799618-53002783	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52835400-52838800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:52835600-52838800	Weak transcription	H1 Cell Line	embryonic stem cell

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