Variant report

Variant	rs12590404
Chromosome Location	chr14:69331653-69331654
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	chr14:69329871..69332801-chr14:69360773..69363561,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12586591	0.93[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap]
rs12588891	0.84[EUR][1000 genomes]
rs1475033	0.87[EUR][1000 genomes]
rs15993	0.89[CHD][hapmap];0.82[MEX][hapmap]
rs17106413	0.85[ASN][1000 genomes]
rs17106441	0.84[EUR][1000 genomes]
rs56732174	0.84[ASN][1000 genomes]
rs7149926	0.97[EUR][1000 genomes]
rs7149929	0.82[ASN][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	nsv1035267	chr14:69230254-69348126	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv542123	chr14:69230254-69348126	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	nsv518793	chr14:69329149-69331653	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12590404	RAB15	cis	parietal	SCAN
rs12590404	KIAA0247	cis	lymphoblastoid	seeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69310800-69332200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr14:69310800-69332200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr14:69310800-69336400	Weak transcription	NHLF	lung
4	chr14:69310800-69339800	Weak transcription	Right Ventricle	heart
5	chr14:69312000-69332000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr14:69320600-69334400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr14:69320800-69332200	Weak transcription	NHEK	skin
8	chr14:69321200-69332200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr14:69321200-69338000	Weak transcription	Gastric	stomach
10	chr14:69322400-69336600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr14:69323800-69337800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr14:69324800-69338600	Weak transcription	HepG2	liver
13	chr14:69327600-69332200	Weak transcription	Liver	Liver
14	chr14:69328000-69334000	Weak transcription	NH-A	brain
15	chr14:69328200-69336600	Weak transcription	HMEC	breast
16	chr14:69328800-69336200	Weak transcription	HSMM	muscle
17	chr14:69329600-69332400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr14:69329600-69338200	Weak transcription	Pancreas	Pancrea
19	chr14:69330000-69332000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr14:69330000-69332200	Weak transcription	A549	lung
21	chr14:69330000-69338400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr14:69330000-69351000	Weak transcription	Fetal Heart	heart
23	chr14:69330200-69332400	Weak transcription	HUVEC	blood vessel
24	chr14:69330200-69338000	Weak transcription	Hela-S3	cervix
25	chr14:69330200-69338200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr14:69330200-69348200	Weak transcription	K562	blood
27	chr14:69330800-69332000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr14:69331000-69332000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr14:69331000-69332200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr14:69331000-69332400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr14:69331000-69332400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr14:69331000-69332800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr14:69331000-69332800	Strong transcription	HSMMtube	muscle
34	chr14:69331200-69331800	ZNF genes & repeats	Fetal Stomach	stomach
35	chr14:69331200-69332200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr14:69331200-69332800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr14:69331200-69332800	Strong transcription	Osteobl	bone
38	chr14:69331200-69338200	Weak transcription	Colonic Mucosa	Colon
39	chr14:69331200-69350800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr14:69331400-69332200	Weak transcription	Aorta	Aorta
41	chr14:69331400-69332800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
42	chr14:69331400-69344600	Weak transcription	Brain Angular Gyrus	brain
43	chr14:69331600-69331800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
44	chr14:69331600-69332800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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