Variant report

Variant	rs17166655
Chromosome Location	chr7:13086461-13086462
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:13085851..13087402-chr7:13106082..13107771,2	K562	blood:
2	chr7:12726944..12729146-chr7:13085985..13088167,2	K562	blood:
3	chr7:13081390..13084291-chr7:13084595..13087584,2	K562	blood:

Variant related genes	Relation type
ENSG00000122644	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10488243	0.82[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap]
rs10950431	0.82[EUR][1000 genomes]
rs10950432	0.82[EUR][1000 genomes]
rs10950433	0.82[EUR][1000 genomes]
rs10950434	0.82[EUR][1000 genomes]
rs11975327	0.81[CEU][hapmap];0.86[JPT][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11983822	0.82[EUR][1000 genomes]
rs12056050	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12056168	0.82[EUR][1000 genomes]
rs12056220	0.83[EUR][1000 genomes]
rs12113090	0.82[CEU][hapmap];0.84[GIH][hapmap]
rs12531362	0.82[CEU][hapmap]
rs12531363	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs12533128	0.83[EUR][1000 genomes]
rs12534513	0.81[EUR][1000 genomes]
rs12534537	0.82[EUR][1000 genomes]
rs12534546	0.82[EUR][1000 genomes]
rs12536140	0.87[EUR][1000 genomes]
rs12536193	0.87[EUR][1000 genomes]
rs12539699	0.82[EUR][1000 genomes]
rs12672647	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17166612	0.84[EUR][1000 genomes]
rs17166626	0.88[EUR][1000 genomes]
rs17166651	0.90[EUR][1000 genomes]
rs17166653	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17166658	0.90[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17166671	0.90[ASW][hapmap];0.87[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs17166673	0.83[JPT][hapmap]
rs17166674	0.87[EUR][1000 genomes]
rs17166689	0.87[EUR][1000 genomes]
rs17166711	0.83[EUR][1000 genomes]
rs17166756	0.81[CEU][hapmap]
rs1861237	0.81[EUR][1000 genomes]
rs1981639	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs2005878	0.87[EUR][1000 genomes]
rs2006291	0.88[EUR][1000 genomes]
rs2160193	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2191043	0.82[CEU][hapmap]
rs28639785	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs34125302	0.83[EUR][1000 genomes]
rs34404228	0.87[EUR][1000 genomes]
rs34932308	0.87[EUR][1000 genomes]
rs35023832	0.87[EUR][1000 genomes]
rs35432593	0.87[EUR][1000 genomes]
rs4636097	0.87[AFR][1000 genomes]
rs4719347	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4721177	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs60705466	0.83[EUR][1000 genomes]
rs6460997	0.83[EUR][1000 genomes]
rs6949649	0.83[EUR][1000 genomes]
rs6950752	0.80[EUR][1000 genomes]
rs6956549	0.90[EUR][1000 genomes]
rs6964875	0.85[CEU][hapmap]
rs6969769	0.86[EUR][1000 genomes]
rs6974627	0.81[CEU][hapmap]
rs6977552	0.90[EUR][1000 genomes]
rs73261908	0.83[EUR][1000 genomes]
rs73261923	0.85[EUR][1000 genomes]
rs73261936	0.96[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs73261949	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73261950	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73261964	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs73261983	0.87[EUR][1000 genomes]
rs736198	0.83[EUR][1000 genomes]
rs7778887	0.83[EUR][1000 genomes]
rs7788484	0.82[CEU][hapmap]
rs7789528	0.87[EUR][1000 genomes]
rs7789970	0.82[CEU][hapmap]
rs7790328	0.82[CEU][hapmap]
rs7790665	0.82[CEU][hapmap]
rs7793405	0.86[EUR][1000 genomes]
rs7793573	0.82[EUR][1000 genomes]
rs7799356	0.81[CEU][hapmap]
rs9639142	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
6	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
7	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
8	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
9	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17166655	ARL4A	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:13082800-13089800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr7:13083200-13089400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr7:13084800-13086600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:13085800-13086600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:13085800-13086800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:13085800-13089400	Weak transcription	NHLF	lung
7	chr7:13086000-13089200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr7:13086000-13089400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr7:13086400-13086600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:13086400-13086600	Flanking Active TSS	A549	lung
11	chr7:13086400-13087200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links