Variant report

Variant	rs1538544
Chromosome Location	chr1:215429425-215429426
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10864165	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10864166	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10864169	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11120519	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs11120524	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11120530	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11120533	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120539	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11120541	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11120542	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11120581	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap]
rs11583745	0.92[CEU][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11588455	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12026669	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12026702	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12037855	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038616	0.84[CEU][hapmap]
rs12038695	0.84[CEU][hapmap];0.83[CHD][hapmap]
rs12044688	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12047082	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12049601	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12407482	0.90[EUR][1000 genomes]
rs12739619	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12740245	0.88[CEU][hapmap]
rs12750276	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12752882	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12753507	0.88[CEU][hapmap]
rs1339401	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1416653	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1416654	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1416655	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1416661	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1538547	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs17024500	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs2153244	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3933352	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4098470	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4098471	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4233309	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap]
rs4281301	0.83[AFR][1000 genomes]
rs4446938	0.81[ASN][1000 genomes]
rs4655397	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4655398	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4655399	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4655400	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5025775	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs6540886	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6540887	0.96[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6670661	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6674743	0.90[EUR][1000 genomes]
rs7522160	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7522552	0.84[CEU][hapmap]
rs7531046	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs946487	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs946488	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs946489	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs946490	0.94[AMR][1000 genomes];0.97[EUR][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	nsv873169	chr1:215264486-215453286	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
2	nsv873170	chr1:215367248-215440975	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1538544	ESRRG	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215429000-215431800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:215429200-215432800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr1:215429400-215429800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links