Variant report

Variant	rs4975790
Chromosome Location	chr5:2010376-2010377
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs13153217	0.84[ASW][hapmap];1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13162781	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13190594	1.00[CEU][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35375504	0.84[AMR][1000 genomes]
rs4975720	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975778	0.82[CHD][hapmap]
rs4975792	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975794	0.81[MEX][hapmap]
rs730633	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs901499	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs901507	0.90[EUR][1000 genomes]
rs9312971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv915846	chr5:1891098-2167677	Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1026930	chr5:1898993-2126061	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv427705	chr5:1950467-2115059	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4975790	BRD9	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:2007400-2011800	Enhancers	Fetal Heart	heart
2	chr5:2008600-2012000	Weak transcription	Right Atrium	heart
3	chr5:2008800-2010400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr5:2008800-2011600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:2008800-2013200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:2009000-2011800	Weak transcription	NHEK	skin
7	chr5:2009000-2013200	Weak transcription	HMEC	breast
8	chr5:2009200-2010800	Enhancers	Dnd41	blood
9	chr5:2009200-2011600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:2009400-2011200	Weak transcription	Left Ventricle	heart
11	chr5:2009400-2012000	Weak transcription	Right Ventricle	heart
12	chr5:2009400-2014400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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

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