Variant report

Variant	rs13291971
Chromosome Location	chr9:12861065-12861066
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:12776291..12778540-chr9:12858744..12861808,3	MCF-7	breast:
2	chr9:12774993..12776787-chr9:12859999..12861752,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153714	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10491739	0.86[EUR][1000 genomes]
rs10491740	0.80[EUR][1000 genomes]
rs13285285	0.94[EUR][1000 genomes]
rs13291898	0.94[CEU][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes]
rs16923061	0.80[EUR][1000 genomes]
rs471329	0.80[ASN][1000 genomes]
rs474762	0.86[ASN][1000 genomes]
rs491308	0.90[ASN][1000 genomes]
rs491969	0.90[ASN][1000 genomes]
rs492198	0.90[ASN][1000 genomes]
rs504466	0.84[ASN][1000 genomes]
rs551528	0.87[ASN][1000 genomes]
rs551617	0.90[ASN][1000 genomes]
rs579723	0.84[ASN][1000 genomes]
rs639917	0.89[ASN][1000 genomes]
rs642563	0.90[ASN][1000 genomes]
rs6474741	0.84[JPT][hapmap];1.00[MEX][hapmap]
rs655155	0.90[ASN][1000 genomes]
rs656951	0.86[ASN][1000 genomes]
rs656954	0.88[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13291971	PRKAB1	trans	brain	seeQTL
rs13291971	ZFYVE1	trans	brain	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12851800-12867000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:12857000-12862400	Weak transcription	Fetal Kidney	kidney
3	chr9:12857200-12862800	Weak transcription	Fetal Lung	lung
4	chr9:12858800-12861200	Enhancers	NHEK	skin
5	chr9:12859200-12861200	Enhancers	NHDF-Ad	bronchial
6	chr9:12859200-12864600	Enhancers	Fetal Intestine Small	intestine
7	chr9:12859400-12864400	Enhancers	Fetal Intestine Large	intestine
8	chr9:12859600-12864000	Weak transcription	Small Intestine	intestine
9	chr9:12859800-12862400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:12860000-12861400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:12860000-12861400	Enhancers	Hela-S3	cervix
12	chr9:12860000-12861600	Enhancers	Duodenum Mucosa	Duodenum
13	chr9:12860200-12862600	Weak transcription	NHLF	lung
14	chr9:12860400-12861200	Enhancers	NH-A	brain
15	chr9:12860400-12861400	Enhancers	A549	lung
16	chr9:12860400-12861400	Enhancers	Osteobl	bone
17	chr9:12860600-12861400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:12860600-12861400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:12860600-12861600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:12860800-12861200	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr9:12860800-12861200	Enhancers	Stomach Mucosa	stomach
22	chr9:12860800-12861400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:12860800-12861400	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr9:12860800-12861400	Enhancers	HMEC	breast
25	chr9:12861000-12861200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr9:12861000-12861200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:12861000-12861200	ZNF genes & repeats	Aorta	Aorta
28	chr9:12861000-12861400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:12861000-12861800	Enhancers	Pancreas	Pancrea
30	chr9:12861000-12862800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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