Variant report

Variant	rs162538
Chromosome Location	chr21:28275461-28275462
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1497288	1.00[ASN][1000 genomes]
rs151056	0.83[EUR][1000 genomes]
rs162488	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162490	0.87[CEU][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162491	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162492	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162493	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162496	0.84[CEU][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs162497	0.84[CEU][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs162498	0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162499	0.84[CEU][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs162501	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs162503	1.00[ASN][1000 genomes]
rs162504	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs162505	1.00[ASN][1000 genomes]
rs162506	0.80[TSI][hapmap]
rs162507	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs162508	1.00[ASN][1000 genomes]
rs162510	0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];1.00[ASN][1000 genomes]
rs162516	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162520	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162521	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162531	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162532	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs162533	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162534	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162535	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162536	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162537	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162539	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162540	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162541	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229045	0.84[EUR][1000 genomes]
rs229046	0.84[EUR][1000 genomes]
rs229053	1.00[JPT][hapmap]
rs229060	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229061	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229063	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229064	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229069	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229071	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229076	0.96[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229078	0.91[CEU][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229079	0.88[CEU][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs229085	1.00[ASN][1000 genomes]
rs229087	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229088	0.96[CEU][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229089	0.96[CEU][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs229090	0.84[EUR][1000 genomes]
rs229091	0.91[CEU][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs229093	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229095	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229097	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229103	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229109	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs229110	0.91[EUR][1000 genomes]
rs233899	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233900	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2830556	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2830558	0.84[EUR][1000 genomes]
rs2830584	0.84[EUR][1000 genomes]
rs2830589	0.83[CEU][hapmap]
rs389125	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs431134	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs457947	1.00[ASN][1000 genomes]
rs4817147	1.00[ASN][1000 genomes]
rs7281968	0.84[EUR][1000 genomes]
rs73358063	1.00[ASN][1000 genomes]
rs73358075	1.00[ASN][1000 genomes]
rs73899348	1.00[ASN][1000 genomes]
rs8127064	1.00[ASN][1000 genomes]
rs8131204	1.00[ASN][1000 genomes]
rs8992	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9647124	1.00[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	nsv1066573	chr21:28096356-28374354	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1057400	chr21:28104936-28359948	Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv834068	chr21:28179670-28360808	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1067475	chr21:28238746-29046707	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28273800-28276000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr21:28274800-28276400	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr21:28274800-28276600	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr21:28275000-28276000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr21:28275000-28276400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links