Variant report

Variant	rs9450619
Chromosome Location	chr6:87827827-87827828
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1145712	0.88[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap]
rs1145714	0.92[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap]
rs1145715	0.92[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap]
rs1203162	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap]
rs1203163	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs1203164	0.88[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap]
rs13201289	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes]
rs13210074	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16878497	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1925686	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1925689	0.81[CEU][hapmap]
rs2025490	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2147917	0.81[CEU][hapmap]
rs2147918	0.81[CEU][hapmap]
rs242263	0.87[CHB][hapmap];0.98[CHD][hapmap];0.85[JPT][hapmap]
rs368267	0.92[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs3734187	0.81[CEU][hapmap]
rs3812130	0.81[CEU][hapmap]
rs3846776	0.81[CEU][hapmap]
rs3857483	0.84[CEU][hapmap]
rs3857484	0.81[CEU][hapmap]
rs3999791	0.85[EUR][1000 genomes]
rs4099964	0.81[CEU][hapmap]
rs410683	0.91[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap]
rs411606	0.92[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap]
rs413687	0.92[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs414453	0.92[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs4235830	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs440296	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs4707344	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4707345	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4707348	0.81[CEU][hapmap]
rs4707355	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs6907805	0.81[CEU][hapmap]
rs6908834	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6913159	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6913932	0.81[CEU][hapmap]
rs6921007	0.81[CEU][hapmap]
rs6921673	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs6926686	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs6927748	0.82[CEU][hapmap]
rs6932641	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs6933046	0.81[CEU][hapmap]
rs6934603	0.81[CEU][hapmap]
rs6938885	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap]
rs6939075	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs6940325	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs6940544	0.80[CEU][hapmap]
rs7752414	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs7755883	0.81[CEU][hapmap]
rs7757330	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7767245	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7774603	0.81[CEU][hapmap]
rs912815	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9294375	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9294376	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs9344691	0.85[CEU][hapmap]
rs9344695	0.81[CEU][hapmap]
rs9353468	0.81[CEU][hapmap]
rs9359743	0.81[CEU][hapmap]
rs9362411	0.81[CEU][hapmap]
rs9362415	0.81[CEU][hapmap]
rs9444476	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9444481	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9444486	0.80[EUR][1000 genomes]
rs9444488	0.81[EUR][1000 genomes]
rs9444491	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9450623	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9450630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9450636	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs9450637	0.81[EUR][1000 genomes]
rs9450638	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs9450639	0.84[EUR][1000 genomes]
rs9450650	0.81[CEU][hapmap]
rs9450651	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs9450652	0.81[CEU][hapmap]
rs9450653	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.80[LWK][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024751	chr6:87433199-87908721	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv604114	chr6:87816905-87906053	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2758067	chr6:87817883-87992957	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv2759453	chr6:87817883-87992957	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9450619	SLC35A1	cis	parietal	SCAN
rs9450619	ZNF292	cis	Lymphoblastoid	GTEx
rs9450619	C6orf162	cis	cerebellum	SCAN
rs9450619	C6orf163	cis	parietal	SCAN
rs9450619	Hs.485895	cis	multi-tissue	Pritchard
rs9450619	C6orf162	cis	parietal	SCAN
rs9450619	MDN1	cis	parietal	SCAN
rs9450619	C6orf162	cis	multi-tissue	Pritchard

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87827400-87828200	Enhancers	HMEC	breast
2	chr6:87827400-87830000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:87827600-87828200	Enhancers	Hela-S3	cervix
4	chr6:87827600-87828400	Enhancers	NHEK	skin
5	chr6:87827800-87828400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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