Variant report

Variant	rs12534537
Chromosome Location	chr7:13043413-13043414
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10488243	0.95[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.83[ASN][1000 genomes]
rs10950428	0.88[ASN][1000 genomes]
rs11975327	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12112648	0.90[ASN][1000 genomes]
rs12113090	0.87[CEU][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap]
rs12530565	0.88[ASN][1000 genomes]
rs12530643	0.86[ASN][1000 genomes]
rs12530651	0.86[ASN][1000 genomes]
rs12531362	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs12531363	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs12532653	0.82[ASN][1000 genomes]
rs12537378	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12537712	0.92[ASN][1000 genomes]
rs12671480	0.90[ASN][1000 genomes]
rs12672647	0.91[ASN][1000 genomes]
rs17166605	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17166608	0.92[ASN][1000 genomes]
rs17166610	0.92[ASN][1000 genomes]
rs17166612	0.92[ASN][1000 genomes]
rs17166614	0.92[ASN][1000 genomes]
rs17166626	0.90[ASN][1000 genomes]
rs17166643	0.87[ASN][1000 genomes]
rs17166651	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17166653	0.90[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap]
rs17166655	1.00[ASW][hapmap];0.94[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs17166658	0.90[ASW][hapmap];0.81[CEU][hapmap];0.94[GIH][hapmap]
rs17166671	0.90[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs17166673	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs17166756	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs1861237	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1981639	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs2110650	0.86[ASN][1000 genomes]
rs2160193	0.80[EUR][1000 genomes]
rs2191043	0.87[CEU][hapmap];0.83[JPT][hapmap]
rs2215950	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28639785	0.80[EUR][1000 genomes]
rs34125302	0.84[ASN][1000 genomes]
rs4236278	0.80[CEU][hapmap];0.91[JPT][hapmap]
rs4636097	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4719347	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4721177	0.92[ASN][1000 genomes]
rs55957561	0.91[ASN][1000 genomes]
rs57459966	0.88[ASN][1000 genomes]
rs59675898	0.88[ASN][1000 genomes]
rs60020188	0.86[ASN][1000 genomes]
rs60345281	0.92[ASN][1000 genomes]
rs60705466	0.90[ASN][1000 genomes]
rs61232028	0.92[ASN][1000 genomes]
rs61639094	0.86[ASN][1000 genomes]
rs6461007	0.91[JPT][hapmap]
rs6950438	0.92[ASN][1000 genomes]
rs6950752	0.92[ASN][1000 genomes]
rs6956549	0.92[ASN][1000 genomes]
rs6964875	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs6974627	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs6977552	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73259988	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73259991	0.85[ASN][1000 genomes]
rs73261908	0.89[ASN][1000 genomes]
rs73261911	0.90[ASN][1000 genomes]
rs73261913	0.89[ASN][1000 genomes]
rs73261923	0.90[ASN][1000 genomes]
rs73261936	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73261949	0.81[EUR][1000 genomes]
rs73261954	0.83[ASN][1000 genomes]
rs73261964	0.84[ASN][1000 genomes]
rs738052	0.92[ASN][1000 genomes]
rs763534	0.86[ASN][1000 genomes]
rs7777911	0.88[ASN][1000 genomes]
rs7778632	0.88[ASN][1000 genomes]
rs7787998	0.85[ASN][1000 genomes]
rs7788484	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs7789970	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs7790328	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs7790665	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs7790770	0.84[CEU][hapmap];0.91[JPT][hapmap]
rs7797104	0.88[ASN][1000 genomes]
rs7799356	0.86[CEU][hapmap]
rs9639142	0.87[CEU][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12534537	ARL4A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:13036800-13049000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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