Variant report

Variant	rs2309586
Chromosome Location	chr2:100137660-100137661
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1000409	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10170425	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10172068	0.92[CEU][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10172752	0.92[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10173466	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10186340	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10187843	0.92[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10205985	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123786	0.92[CEU][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11679115	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11683651	0.92[CEU][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11687870	0.88[CEU][hapmap];0.84[YRI][hapmap]
rs11887109	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11887574	0.89[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11902994	0.92[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12464535	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12478488	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12621141	0.80[AMR][1000 genomes]
rs12623540	0.92[CEU][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13017871	0.89[CEU][hapmap];0.84[YRI][hapmap]
rs13018274	0.89[CEU][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.84[YRI][hapmap]
rs13384883	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13389623	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13392042	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13394688	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13427780	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1376443	0.81[AMR][1000 genomes]
rs1451243	0.92[CEU][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1901283	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2242037	0.89[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2290256	0.92[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2305354	0.92[CEU][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2309585	0.89[CEU][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28369943	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28382954	0.84[AMR][1000 genomes]
rs3087386	0.92[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3792134	0.89[CEU][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3792146	0.92[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3792149	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3792152	0.86[GIH][hapmap];0.85[TSI][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3811555	0.92[CEU][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes]
rs3828316	0.92[CEU][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4535093	0.92[CEU][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4850901	0.88[CEU][hapmap];0.84[YRI][hapmap]
rs4850903	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4851205	0.92[CEU][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6542879	0.92[CEU][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6542880	0.92[CEU][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6542882	0.92[CEU][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6706607	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6708861	0.92[CEU][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes]
rs6713792	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6714244	0.92[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6717515	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6721297	0.84[CEU][hapmap]
rs6734290	0.89[CEU][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.84[YRI][hapmap];0.80[AMR][1000 genomes]
rs7558074	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7561079	0.92[CEU][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7567674	0.92[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7571202	0.92[CEU][hapmap];0.84[YRI][hapmap];0.80[AMR][1000 genomes]
rs7574135	0.92[CEU][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7579403	0.92[CEU][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7580448	0.92[CEU][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7585721	0.92[CEU][hapmap];0.87[TSI][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7586892	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7587419	0.92[CEU][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7591212	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7594838	0.92[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap]
rs7598629	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7601470	0.92[CEU][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7601730	0.92[CEU][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs959929	0.92[CEU][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.88[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	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2309586	FAHD2A	cis	cerebellum	SCAN
rs2309586	LIPT1	cis	cerebellum	SCAN
rs2309586	LYG1	cis	Skin Sun Exposed Lower leg	GTEx
rs2309586	TSGA10	cis	cerebellum	SCAN
rs2309586	LIPT1	cis	parietal	SCAN
rs2309586	TSGA10	cis	multi-tissue	Pritchard
rs2309586	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs2309586	REV1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100136200-100140600	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links