Variant report

Variant	rs2566531
Chromosome Location	chr2:133435305-133435306
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:133424851..133426510-chr2:133433798..133435548,2	MCF-7	breast:
2	chr2:133430925..133433082-chr2:133435117..133437113,2	K562	blood:
3	chr2:133426909..133430819-chr2:133431884..133436049,6	MCF-7	breast:
4	chr2:133430145..133433082-chr2:133435117..133437430,2	K562	blood:
5	chr2:133426594..133429327-chr2:133434944..133438261,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150551	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs13028563	0.80[JPT][hapmap]
rs1430630	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1430631	0.96[CEU][hapmap];0.87[CHB][hapmap];0.80[JPT][hapmap];0.97[EUR][1000 genomes]
rs1430632	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17396523	0.80[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs17396537	0.84[ASW][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs17396607	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1897166	0.85[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2033332	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2082177	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2082179	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2082181	0.95[CEU][hapmap];0.87[CHB][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2163342	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2244888	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2248193	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2250481	0.83[CEU][hapmap]
rs2288653	0.95[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2315599	0.81[JPT][hapmap]
rs2435612	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2566525	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2566528	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2566529	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2566530	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2566535	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2566536	0.96[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2566537	0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2566538	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2709520	0.96[CEU][hapmap];0.87[CHB][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2709521	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2709523	0.91[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2709524	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2709525	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2709526	0.94[EUR][1000 genomes]
rs2709527	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2709528	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2709532	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2709533	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2709534	0.92[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2709536	0.92[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs2709541	0.83[EUR][1000 genomes]
rs2709542	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2709545	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2709546	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2709548	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2709549	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4954351	0.81[JPT][hapmap]
rs4954352	0.81[JPT][hapmap]
rs713535	0.96[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs721470	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs744821	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9973717	0.81[JPT][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	nsv1011421	chr2:132895241-133682185	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv875137	chr2:133167263-133714142	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv583158	chr2:133316092-133862100	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv875138	chr2:133410921-133761794	Enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2566531	IMP4	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133429200-133439400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:133430000-133444000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:133430800-133439400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:133434600-133437000	Enhancers	NH-A	brain
5	chr2:133435000-133435400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:133435000-133436200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:133435200-133435400	Flanking Active TSS	Osteobl	bone

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