Variant report

Variant	rs663521
Chromosome Location	chr1:84530053-84530054
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:84528524..84531344-chr1:84538975..84541375,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1016379	1.00[ASW][hapmap];0.95[CHD][hapmap];0.82[ASN][1000 genomes]
rs12031206	0.82[ASN][1000 genomes]
rs12035258	1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs1811643	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2139931	0.86[ASW][hapmap];0.95[CHD][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs2642181	0.82[ASN][1000 genomes]
rs2642182	0.86[ASW][hapmap];0.82[ASN][1000 genomes]
rs2642184	1.00[ASW][hapmap];0.91[CHD][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs2642185	0.86[ASW][hapmap];0.91[CHD][hapmap];0.85[YRI][hapmap]
rs2684911	0.86[ASW][hapmap];0.91[CHD][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs2684914	1.00[ASW][hapmap];0.91[CHD][hapmap];0.82[ASN][1000 genomes]
rs2811999	0.82[ASN][1000 genomes]
rs2812447	0.85[YRI][hapmap]
rs2812451	0.83[CHB][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs2892811	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs481354	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs512737	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs523531	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs532246	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs562971	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs566830	0.87[ASN][1000 genomes]
rs592905	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs597594	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs615352	0.83[ASN][1000 genomes]
rs618232	0.90[CEU][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap]
rs625107	0.83[ASN][1000 genomes]
rs626376	0.87[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.81[MKK][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs629277	0.83[ASN][1000 genomes]
rs649226	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs659227	0.83[ASN][1000 genomes]
rs659743	0.83[ASN][1000 genomes]
rs667304	1.00[CHB][hapmap]
rs669110	0.83[ASN][1000 genomes]
rs671209	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs678794	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs680627	1.00[JPT][hapmap]
rs680905	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs683074	0.90[CEU][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap]
rs684651	0.83[ASN][1000 genomes]
rs726607	0.86[CEU][hapmap];0.80[MKK][hapmap]
rs72711180	0.82[ASN][1000 genomes]
rs7530801	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs810915	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1732	chr1:84499098-84544635	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv871655	chr1:84517261-84550849	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs663521	ZNF528	trans	parietal	SCAN
rs663521	LPHN2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84528400-84532600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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