Variant report

Variant	rs10489358
Chromosome Location	chr1:168654873-168654874
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10489359	0.81[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10918958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1108637	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588432	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11588434	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11590795	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11799741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094644	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12726636	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12727749	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12745063	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12748015	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12749426	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12749876	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1337747	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1337748	0.85[EUR][1000 genomes]
rs1412334	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1412335	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1412336	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415678	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1415680	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16861287	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17502304	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17502351	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17502574	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17561671	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2223911	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2419126	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2419128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34099957	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35492795	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4437856	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58620990	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688592	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs726055	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7416358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007846	chr1:168449940-168687265	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv831836	chr1:168538779-168716956	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv872530	chr1:168618641-168658544	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1001684	chr1:168636622-168663398	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv525556	chr1:168653857-168662352	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10489358	SELL	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168653200-168655000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:168653400-168656200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:168653400-168656200	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:168653800-168658000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:168654800-168657800	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links