Variant report

Variant	rs17166608
Chromosome Location	chr7:13067198-13067199
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 128 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10488243	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10950428	0.92[ASN][1000 genomes]
rs10950431	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10950432	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10950433	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10950434	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11975327	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11983822	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12056050	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12056168	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12056220	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12112648	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12113090	0.87[CEU][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap]
rs12530565	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12530643	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12530651	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12531362	0.87[CEU][hapmap];0.80[JPT][hapmap]
rs12531363	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs12532653	0.90[ASN][1000 genomes]
rs12533128	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12534513	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12534537	0.92[ASN][1000 genomes]
rs12534546	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12536140	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12536193	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12537378	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12537712	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12539699	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12671480	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12672647	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17166605	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17166610	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17166612	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17166614	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17166626	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17166643	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17166651	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17166653	0.91[ASW][hapmap];0.80[CEU][hapmap];0.97[GIH][hapmap];0.85[LWK][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs17166655	0.82[ASW][hapmap];0.82[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap]
rs17166658	0.91[ASW][hapmap];0.94[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs17166671	0.91[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17166673	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17166674	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17166689	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17166711	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17166756	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs1861237	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1981639	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs2005878	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2006291	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2110650	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2160193	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2191043	0.87[CEU][hapmap]
rs2215950	0.83[ASN][1000 genomes]
rs28639785	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34125302	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34404228	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34932308	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35023832	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35432593	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4236278	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs4636097	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4719347	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4721177	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55957561	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs57459966	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59675898	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60020188	0.90[ASN][1000 genomes]
rs60345281	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60705466	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61232028	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61639094	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6460997	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6461007	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs6949649	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6950122	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6950438	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6950752	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6956549	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6964875	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs6969380	0.81[AMR][1000 genomes]
rs6969769	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6974627	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs6977552	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73259988	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73259991	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73261908	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73261911	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73261913	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73261923	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73261936	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73261954	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73261964	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73261983	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs736198	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs738052	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs763534	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7777911	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7778632	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7778887	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7787776	0.81[AMR][1000 genomes]
rs7787998	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7788257	0.81[AMR][1000 genomes]
rs7788484	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs7789174	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7789528	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7789970	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs7790328	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs7790665	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs7790770	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs7793289	0.82[AMR][1000 genomes]
rs7793405	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7793573	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7797104	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7799356	0.86[CEU][hapmap]
rs9639142	0.87[CEU][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932020	chr7:12676890-13239551	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv868830	chr7:12712753-13517417	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv606235	chr7:12781381-13205950	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1020568	chr7:12802640-13183737	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv464384	chr7:12907178-13077065	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv606238	chr7:12907178-13077065	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1029771	chr7:12927648-13153855	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv538736	chr7:12927648-13153855	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1026624	chr7:12963907-13123408	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv887642	chr7:12973609-13067198	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1019173	chr7:13063854-13585360	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv538737	chr7:13063854-13585360	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17166608	ARL4A	cis	parietal	SCAN
rs17166608	TSPAN13	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:13059000-13068000	Weak transcription	A549	lung
2	chr7:13062200-13071200	Weak transcription	HepG2	liver
3	chr7:13063800-13068600	Weak transcription	Brain Germinal Matrix	brain
4	chr7:13064200-13067800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:13064400-13068000	Weak transcription	HMEC	breast
6	chr7:13064400-13068200	Weak transcription	Fetal Lung	lung
7	chr7:13066400-13068600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr7:13067000-13067200	Enhancers	Fetal Kidney	kidney
9	chr7:13067000-13068800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links