Variant report

Variant	rs9496238
Chromosome Location	chr6:142369802-142369803
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11758623	0.90[JPT][hapmap]
rs178783	0.90[JPT][hapmap]
rs225604	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs225605	0.88[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap]
rs225606	1.00[ASW][hapmap];0.88[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs225618	0.83[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap]
rs225620	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs225622	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs225623	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs225624	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs225629	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs225630	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap]
rs225631	0.88[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap]
rs225632	0.88[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap]
rs225633	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs225634	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs225635	1.00[ASW][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap]
rs225639	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs225641	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs225642	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs225643	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs225652	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs225653	1.00[ASW][hapmap];0.81[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap]
rs225654	1.00[ASW][hapmap];0.81[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap]
rs225656	0.90[JPT][hapmap]
rs225657	0.90[JPT][hapmap]
rs225658	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs225659	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs225660	0.81[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap]
rs225662	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs225663	0.81[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap]
rs225665	0.91[ASW][hapmap];0.81[CEU][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.84[MKK][hapmap];0.84[YRI][hapmap]
rs225666	0.90[JPT][hapmap]
rs225671	0.90[GIH][hapmap];0.90[JPT][hapmap]
rs225673	0.90[JPT][hapmap]
rs225674	0.90[JPT][hapmap]
rs225675	0.90[JPT][hapmap]
rs225676	0.86[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap]
rs225677	0.88[JPT][hapmap]
rs225678	0.89[JPT][hapmap]
rs225679	0.90[JPT][hapmap]
rs225684	0.90[GIH][hapmap];0.90[JPT][hapmap]
rs225685	0.90[JPT][hapmap]
rs225687	0.90[JPT][hapmap]
rs225688	0.90[JPT][hapmap]
rs225689	0.90[JPT][hapmap]
rs225695	0.90[JPT][hapmap]
rs225700	0.90[JPT][hapmap]
rs225701	0.88[JPT][hapmap]
rs225702	0.90[JPT][hapmap]
rs225710	0.90[GIH][hapmap];0.90[JPT][hapmap]
rs4352696	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4407737	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4631307	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4896570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896574	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4896575	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs62430456	0.81[ASN][1000 genomes]
rs628311	1.00[ASW][hapmap];0.88[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap]
rs639658	1.00[ASW][hapmap];0.88[CEU][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap]
rs6570491	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6907175	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7774914	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7776318	0.90[JPT][hapmap]
rs9373335	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496219	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv604792	chr6:142192725-142399251	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1019170	chr6:142234933-142397088	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv886732	chr6:142290338-142536049	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv886733	chr6:142316672-142514226	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' 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
5	nsv464069	chr6:142322456-142407741	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv604794	chr6:142322456-142407741	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1027489	chr6:142336722-142429903	Bivalent Enhancer Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv886734	chr6:142347611-142523865	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv830824	chr6:142361107-142544929	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv886735	chr6:142365171-142472294	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv886736	chr6:142365171-142523865	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9496238	VTA1	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142362200-142376600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:142367200-142370600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:142369600-142370000	Active TSS	Brain Angular Gyrus	brain

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