Variant report

Variant	rs12546288
Chromosome Location	chr8:40009304-40009305
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	chr8:40007975..40009523-chr8:40010479..40012252,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176907	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10103059	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11780250	0.98[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12541392	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12548579	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28398043	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28687838	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4398898	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6983906	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7814906	0.82[AFR][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	nsv539555	chr8:39683857-40673606	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv534582	chr8:39884590-40653224	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:40003000-40009400	Weak transcription	Fetal Kidney	kidney
2	chr8:40003800-40010000	Weak transcription	Fetal Stomach	stomach
3	chr8:40006600-40010000	Enhancers	Placenta Amnion	Placenta Amnion
4	chr8:40007000-40009400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr8:40008000-40010400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr8:40008800-40009600	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr8:40009000-40009400	Enhancers	Liver	Liver
8	chr8:40009000-40009600	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr8:40009000-40009800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr8:40009000-40010000	Enhancers	A549	lung
11	chr8:40009000-40010200	Enhancers	HepG2	liver
12	chr8:40009000-40010600	Enhancers	Fetal Intestine Small	intestine
13	chr8:40009000-40010800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr8:40009200-40009400	Enhancers	Small Intestine	intestine
15	chr8:40009200-40009600	Flanking Active TSS	Colon Smooth Muscle	Colon
16	chr8:40009200-40009600	Enhancers	Lung	lung
17	chr8:40009200-40009600	Enhancers	Ovary	ovary
18	chr8:40009200-40009600	Flanking Active TSS	Rectal Smooth Muscle	rectum
19	chr8:40009200-40010000	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr8:40009200-40010000	Enhancers	Right Atrium	heart
21	chr8:40009200-40010200	Enhancers	Pancreas	Pancrea
22	chr8:40009200-40010200	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr8:40009200-40010400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr8:40009200-40010400	Enhancers	Fetal Lung	lung
25	chr8:40009200-40010600	Enhancers	Hela-S3	cervix
26	chr8:40009200-40010800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr8:40009200-40010800	Enhancers	Stomach Mucosa	stomach
28	chr8:40009200-40011000	Enhancers	Fetal Intestine Large	intestine

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