Variant report

Variant	rs13189629
Chromosome Location	chr5:52078823-52078824
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10512992	0.89[CHB][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.83[ASN][1000 genomes]
rs10940270	0.89[ASW][hapmap]
rs12652120	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12653042	0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13158244	1.00[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13182946	0.96[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13188662	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2454581	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2938796	0.96[CEU][hapmap];0.98[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6879140	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6883810	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754787	chr5:51688543-52193243	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv1027410	chr5:52022713-52103360	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1024123	chr5:52052104-52089545	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1020640	chr5:52058830-52120858	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13189629	BAT2L1	trans	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52075000-52080400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr5:52077800-52080000	Enhancers	HSMMtube	muscle
3	chr5:52078400-52079400	Enhancers	NHDF-Ad	bronchial
4	chr5:52078400-52080200	Enhancers	Hela-S3	cervix
5	chr5:52078600-52079400	Enhancers	Small Intestine	intestine
6	chr5:52078600-52080000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:52078600-52080000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:52078600-52080200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:52078800-52079400	Enhancers	Muscle Satellite Cultured Cells	--
10	chr5:52078800-52079800	Enhancers	NHLF	lung
11	chr5:52078800-52080000	Enhancers	HSMM	muscle

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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