Variant report

Variant	rs517412
Chromosome Location	chr1:57560649-57560650
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs34867472	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs472811	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs485090	0.91[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs486736	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs493334	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs496780	0.92[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs516494	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs517051	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs517291	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs517794	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs518258	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs521147	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs531729	0.92[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs543144	0.81[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs549528	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs559871	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs564616	0.91[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs567862	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs570011	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs575163	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59491159	0.81[EUR][1000 genomes];0.85[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	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv428752	chr1:57455083-57605082	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs517412	TMEM59	cis	parietal	SCAN
rs517412	BSND	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57548800-57566600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:57549600-57566600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:57551400-57622000	Weak transcription	Fetal Intestine Small	intestine
4	chr1:57556800-57568800	Weak transcription	Right Atrium	heart
5	chr1:57558000-57564800	Weak transcription	Fetal Intestine Large	intestine
6	chr1:57559000-57568600	Weak transcription	Left Ventricle	heart
7	chr1:57560000-57562600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:57560200-57561000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:57560200-57561200	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links