Variant report

Variant	rs7530245
Chromosome Location	chr1:227032528-227032529
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	chr1:227031005..227032884-chr1:227503623..227506611,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1046240	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1150897	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1150900	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11802358	0.80[ASN][1000 genomes]
rs12086302	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12758915	0.83[EUR][1000 genomes]
rs1289395	0.81[EUR][1000 genomes]
rs1289396	0.89[AMR][1000 genomes]
rs1295638	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1295641	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1295643	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1295647	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1296171	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1794038	0.83[EUR][1000 genomes]
rs2073489	0.88[ASN][1000 genomes]
rs2236914	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2236915	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2246221	0.81[EUR][1000 genomes]
rs2793461	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2802268	0.82[ASN][1000 genomes]
rs2855559	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2855560	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2855564	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4653470	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6426541	0.85[ASN][1000 genomes]
rs6426547	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6426548	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6674701	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6688068	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6692729	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6697001	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6697431	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6759	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7514364	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7518926	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7530370	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7547071	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8383	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[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	nsv4766	chr1:227025954-227070961	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3381082	chr1:227029266-227059927	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7530245	PSEN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227026800-227034200	Weak transcription	HMEC	breast
2	chr1:227026800-227043800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:227027000-227034400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:227028000-227034200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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