Variant report

Variant	rs9397624
Chromosome Location	chr6:150405696-150405697
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11754434	0.80[EUR][1000 genomes]
rs11754488	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11755079	0.80[EUR][1000 genomes]
rs11756904	0.80[EUR][1000 genomes]
rs11756945	0.80[EUR][1000 genomes]
rs11759611	0.80[EUR][1000 genomes]
rs13201209	0.83[AMR][1000 genomes]
rs13216978	0.80[EUR][1000 genomes]
rs1537649	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2010259	0.95[CHB][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.87[ASN][1000 genomes]
rs2343271	0.86[AFR][1000 genomes]
rs470138	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs612770	0.86[ASN][1000 genomes]
rs7738164	0.80[EUR][1000 genomes]
rs7753353	0.80[EUR][1000 genomes]
rs7765587	0.80[EUR][1000 genomes]
rs7767719	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs789819	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs789824	0.82[EUR][1000 genomes]
rs789825	0.82[EUR][1000 genomes]
rs789826	0.82[EUR][1000 genomes]
rs789827	0.82[EUR][1000 genomes]
rs789828	0.82[EUR][1000 genomes]
rs789829	0.82[EUR][1000 genomes]
rs806072	0.82[EUR][1000 genomes]
rs912558	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs9322242	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9322243	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs932744	0.82[YRI][hapmap]
rs9371701	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9383663	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9397137	0.95[CHB][hapmap];0.80[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9479622	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1026236	chr6:150360882-150408946	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv886770	chr6:150395424-150499889	Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9397624	LRP11	cis	cerebellum	SCAN
rs9397624	LRP11	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150391200-150410000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:150400800-150408400	Weak transcription	NHEK	skin
3	chr6:150401000-150408200	Weak transcription	HMEC	breast
4	chr6:150401000-150408400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:150401000-150408400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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