Variant report

Variant	rs17629918
Chromosome Location	chr5:179869595-179869596
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr5:179869392-179869620	GM12878	blood:	n/a	chr5:179869483-179869494 chr5:179869498-179869509
2	PRDM1	chr5:179869590-179869619	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
RNU6-525P	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10065976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10073273	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11741421	1.00[ASN][1000 genomes]
rs12513508	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12513789	0.96[ASN][1000 genomes]
rs12513814	0.97[ASN][1000 genomes]
rs12513839	0.94[ASN][1000 genomes]
rs12513859	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12514435	0.97[ASN][1000 genomes]
rs12516913	0.96[ASN][1000 genomes]
rs12517962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521524	0.97[ASN][1000 genomes]
rs12522280	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12523225	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13160344	0.97[ASN][1000 genomes]
rs13165116	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13175868	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13175884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13185599	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17080306	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1848479	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1848480	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1976564	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2387192	1.00[ASN][1000 genomes]
rs2387193	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2387194	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2387195	0.98[ASN][1000 genomes]
rs2387196	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2387198	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28635772	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34642261	0.83[ASN][1000 genomes]
rs34741966	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35003375	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35133282	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35145451	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35345767	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35945814	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs36053175	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs36108396	0.81[ASN][1000 genomes]
rs36110953	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4247235	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4267834	0.97[ASN][1000 genomes]
rs4309930	0.97[ASN][1000 genomes]
rs4326107	0.98[ASN][1000 genomes]
rs4498226	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4566753	0.97[ASN][1000 genomes]
rs4700921	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4700922	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4700923	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62406427	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62406428	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62406429	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs67751216	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs67758130	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6872877	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6887857	0.99[ASN][1000 genomes]
rs7356568	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7379521	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7708848	0.94[ASN][1000 genomes]
rs7718615	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs951921	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs951922	0.99[ASN][1000 genomes]
rs951923	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs951924	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
4	nsv830563	chr5:179717693-179898609	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv1031836	chr5:179742033-180676122	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
7	nsv537984	chr5:179742033-180676122	Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
8	nsv949199	chr5:179743553-180696889	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
9	nsv1023537	chr5:179791679-179982822	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv537985	chr5:179791679-179982822	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	esv2752977	chr5:179860394-179885394	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1019519	chr5:179866730-179959408	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv830564	chr5:179867394-180010096	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17629918	SNORD96A	cis	parietal	SCAN
rs17629918	CLK4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179866000-179869800	Enhancers	Placenta	Placenta

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