Variant report

Variant	rs9532436
Chromosome Location	chr13:40365765-40365766
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:40352027..40354218-chr13:40364182..40366415,2	MCF-7	breast:
2	chr13:40359904..40361413-chr13:40364504..40366595,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11147769	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17591231	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17591266	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4133063	0.87[LWK][hapmap]
rs4245396	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4338665	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4403927	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4408422	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4409964	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4941936	0.85[JPT][hapmap]
rs4941939	0.80[CHD][hapmap]
rs4943694	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4943695	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4943696	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7319128	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7325068	0.91[CEU][hapmap];0.89[CHD][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7327824	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7334651	0.91[CEU][hapmap];0.87[JPT][hapmap];0.86[YRI][hapmap];0.81[EUR][1000 genomes]
rs7337585	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7998641	0.81[EUR][1000 genomes]
rs8000009	0.82[YRI][hapmap]
rs8181861	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9315729	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9315730	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9532420	0.80[CHD][hapmap]
rs9532429	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9532432	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9532439	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9548862	0.82[JPT][hapmap]
rs9548863	0.82[JPT][hapmap]
rs9548900	0.80[EUR][1000 genomes]
rs9548901	0.91[CEU][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9548913	0.81[YRI][hapmap]
rs9548916	0.90[CEU][hapmap];0.85[YRI][hapmap];0.81[EUR][1000 genomes]
rs9548917	0.91[CEU][hapmap];0.89[YRI][hapmap];0.80[EUR][1000 genomes]
rs9548918	0.81[EUR][1000 genomes]
rs9548919	0.91[CEU][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs9548920	0.81[EUR][1000 genomes]
rs9548926	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9548928	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9548929	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9548930	0.91[CEU][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9566474	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9576892	0.80[EUR][1000 genomes]
rs9576896	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9576897	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9576898	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9603617	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1054797	chr13:40198744-40618428	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv541755	chr13:40198744-40618428	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv832586	chr13:40222880-40379063	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1040458	chr13:40249387-40638129	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9532436	COG6	Cis_1M	lymphoblastoid	RTeQTL
rs9532436	COG6	cis	Muscle Skeletal	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40364000-40367000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:40364600-40377200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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