Variant report

Variant	rs508803
Chromosome Location	chr9:12857310-12857311
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	chr9:12851201..12854512-chr9:12857301..12860029,3	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1086376	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs473945	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs483855	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs486740	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs489462	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs491154	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs508134	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs514919	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs536375	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs541813	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs541884	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs546228	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs547287	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs584771	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs635655	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs648299	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs662198	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs664346	0.93[EUR][1000 genomes]
rs790279	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][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	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv892573	chr9:12730636-12874703	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv892574	chr9:12754969-12918226	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv613615	chr9:12830070-12947238	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12850400-12859200	Weak transcription	Small Intestine	intestine
2	chr9:12850600-12859000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr9:12851000-12858400	Weak transcription	Stomach Mucosa	stomach
4	chr9:12851800-12867000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:12854600-12859200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr9:12854800-12859400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr9:12854800-12859400	Weak transcription	Fetal Intestine Large	intestine
8	chr9:12854800-12860000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr9:12855000-12859200	Weak transcription	Fetal Intestine Small	intestine
10	chr9:12855200-12859600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr9:12855400-12857800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:12855400-12858200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:12855400-12858400	Weak transcription	HMEC	breast
14	chr9:12855600-12858800	Weak transcription	NHEK	skin
15	chr9:12855600-12859400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:12855600-12859600	Weak transcription	Adipose Nuclei	Adipose
17	chr9:12856800-12860000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr9:12857000-12859800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:12857000-12862400	Weak transcription	Fetal Kidney	kidney
20	chr9:12857200-12859000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:12857200-12859800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr9:12857200-12860000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr9:12857200-12862800	Weak transcription	Fetal Lung	lung

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