Variant report

Variant	rs12531089
Chromosome Location	chr7:108007441-108007442
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107991896..107993618-chr7:108006610..108008809,2	MCF-7	breast:
2	chr7:107997597..108000598-chr7:108005435..108008873,4	MCF-7	breast:
3	chr7:108006947..108010062-chr7:108010245..108014925,5	MCF-7	breast:
4	chr7:108006500..108008005-chr7:108054331..108056945,2	MCF-7	breast:
5	chr7:108000928..108003876-chr7:108005996..108008885,2	MCF-7	breast:
6	chr7:107974565..107976099-chr7:108007204..108009580,2	MCF-7	breast:
7	chr7:107934022..107936872-chr7:108006050..108008513,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266112	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1016149	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12539530	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12539964	0.89[CEU][hapmap];0.85[CHB][hapmap];0.83[EUR][1000 genomes]
rs13230316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13244715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1990712	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs2080489	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2216259	0.90[CEU][hapmap];0.85[CHB][hapmap];0.84[EUR][1000 genomes]
rs2284285	0.81[JPT][hapmap]
rs2284286	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2284287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2284288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2300027	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2395961	0.90[CEU][hapmap];0.85[CHB][hapmap];0.84[EUR][1000 genomes]
rs2395962	0.89[CEU][hapmap];0.85[CHB][hapmap];0.83[EUR][1000 genomes]
rs34294071	0.82[ASN][1000 genomes]
rs34427132	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35669142	0.84[EUR][1000 genomes]
rs36063908	0.83[EUR][1000 genomes]
rs56102707	0.81[EUR][1000 genomes]
rs6948554	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6957056	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6975557	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7804045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[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	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv831090	chr7:107786650-108011196	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv888942	chr7:107893695-108055858	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv888943	chr7:107893695-108058574	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1030425	chr7:107910716-108041036	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107999200-108008800	Weak transcription	Brain Anterior Caudate	brain
2	chr7:107999200-108011200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:107999600-108009000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:108000000-108008400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:108000000-108008400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:108004000-108016600	Weak transcription	Pancreas	Pancrea
7	chr7:108004400-108016600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr7:108007200-108007600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr7:108007200-108007600	Flanking Active TSS	A549	lung
10	chr7:108007200-108008400	Weak transcription	Fetal Brain Male	brain
11	chr7:108007200-108009400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr7:108007400-108009400	Enhancers	HUVEC	blood vessel

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