Variant report

Variant	rs12514628
Chromosome Location	chr5:167736011-167736012
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	chr5:167732969..167736546-chr5:167740901..167744013,5	MCF-7	breast:
2	chr5:167716372..167720995-chr5:167731384..167738008,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113645	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10051069	0.90[EUR][1000 genomes]
rs10475874	0.91[EUR][1000 genomes]
rs12108717	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12517127	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12519918	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522231	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17051843	0.89[EUR][1000 genomes]
rs17632741	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72822615	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72822616	0.81[EUR][1000 genomes]
rs72822619	0.81[EUR][1000 genomes]
rs72822620	0.81[EUR][1000 genomes]
rs72822623	0.81[EUR][1000 genomes]
rs72838320	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72838323	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72838333	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72838335	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs728668	0.81[EUR][1000 genomes]
rs7718390	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7721532	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534607	chr5:167661667-168454396	Active TSS Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv949154	chr5:167691208-168323234	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv5119	chr5:167724987-167766076	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:167727000-167737600	Weak transcription	Brain Anterior Caudate	brain
2	chr5:167727200-167737800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:167727600-167742600	Weak transcription	Fetal Brain Female	brain
4	chr5:167728000-167737800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr5:167729400-167738000	Weak transcription	Colonic Mucosa	Colon
6	chr5:167729400-167740800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:167729400-167741000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:167729400-167741000	Weak transcription	Fetal Lung	lung
9	chr5:167730400-167740800	Weak transcription	HMEC	breast
10	chr5:167730600-167738000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:167730800-167740800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:167731000-167736400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:167731000-167739200	Weak transcription	Hela-S3	cervix
14	chr5:167731000-167741600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:167731600-167738000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:167732800-167737800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr5:167733000-167737800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr5:167733000-167740800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr5:167733200-167738400	Enhancers	Placenta	Placenta
20	chr5:167734000-167738600	Enhancers	Pancreas	Pancrea
21	chr5:167734200-167740800	Weak transcription	NHEK	skin
22	chr5:167734200-167746000	Enhancers	Fetal Intestine Large	intestine
23	chr5:167734400-167737600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr5:167734400-167746600	Enhancers	Fetal Intestine Small	intestine
25	chr5:167734800-167738400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr5:167735000-167736200	Enhancers	Duodenum Mucosa	Duodenum
27	chr5:167735000-167736600	Enhancers	Stomach Mucosa	stomach
28	chr5:167735400-167736200	Enhancers	Small Intestine	intestine
29	chr5:167735400-167736400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:167735600-167736600	Transcr. at gene 5' and 3'	A549	lung
31	chr5:167735800-167736400	Flanking Active TSS	HepG2	liver
32	chr5:167735800-167736600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:167736000-167736400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr5:167736000-167736400	Flanking Active TSS	Liver	Liver
35	chr5:167736000-167736400	Strong transcription	Esophagus	oesophagus
36	chr5:167736000-167736600	Enhancers	Gastric	stomach

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