Variant report

Variant	rs2822629
Chromosome Location	chr21:15734312-15734313
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1040330	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12479	0.86[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13048179	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13048477	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2037941	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2822624	0.96[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2822631	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2822632	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2822636	0.86[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.84[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2822638	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2822642	0.86[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2822644	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2822652	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2822655	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2822662	0.86[GIH][hapmap];0.95[JPT][hapmap]
rs7276170	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7282521	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9305301	0.85[ASN][1000 genomes]
rs9982492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064554	chr21:15676222-15809321	Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1061686	chr21:15724570-15765777	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2822629	HSPA13	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:15731600-15734400	Weak transcription	HUVEC	blood vessel
2	chr21:15731600-15744800	Weak transcription	Hela-S3	cervix
3	chr21:15733400-15734600	Enhancers	HMEC	breast
4	chr21:15733600-15734400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr21:15733600-15734400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr21:15733600-15734600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr21:15733600-15734600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr21:15733600-15735200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr21:15733600-15735200	Enhancers	NHEK	skin
10	chr21:15733800-15734600	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr21:15733800-15734800	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr21:15734000-15734600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr21:15734200-15734800	Enhancers	Primary neutrophils fromperipheralblood	blood

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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