Variant report

Variant	rs4688003
Chromosome Location	chr3:119146159-119146160
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119145344..119146916-chr3:119149020..119151478,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11712863	0.81[EUR][1000 genomes]
rs11713200	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2049756	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2178318	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2282171	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3195852	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35078244	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3772136	0.89[EUR][1000 genomes]
rs3932422	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4687859	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6438532	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6763561	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6797866	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613562	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7629750	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9713715	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9846088	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9851177	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9855347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4688003	POGLUT1	cis	Artery Tibial	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119112000-119147400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:119121200-119150000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:119133800-119147400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:119134200-119148800	Weak transcription	Pancreas	Pancrea
5	chr3:119134600-119147600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:119134800-119147400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:119135000-119147400	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr3:119135000-119147600	Weak transcription	Fetal Thymus	thymus
9	chr3:119135000-119147800	Weak transcription	Placenta	Placenta
10	chr3:119135000-119148000	Weak transcription	Aorta	Aorta
11	chr3:119135200-119149800	Weak transcription	Gastric	stomach
12	chr3:119135400-119147800	Weak transcription	Ovary	ovary
13	chr3:119135400-119148000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:119135400-119150000	Weak transcription	Spleen	Spleen
15	chr3:119137400-119147800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:119137800-119146800	Weak transcription	Osteobl	bone
17	chr3:119138000-119148400	Weak transcription	Fetal Stomach	stomach
18	chr3:119138000-119152400	Weak transcription	Lung	lung
19	chr3:119139400-119147000	Weak transcription	Left Ventricle	heart
20	chr3:119142400-119150800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:119144400-119150400	ZNF genes & repeats	Liver	Liver
22	chr3:119144600-119152000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:119145000-119147800	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
24	chr3:119145400-119148000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:119145400-119149600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:119145600-119147200	ZNF genes & repeats	HUVEC	blood vessel
27	chr3:119145600-119147800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:119145600-119148000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
29	chr3:119145600-119148200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:119145600-119149000	ZNF genes & repeats	HSMM	muscle
31	chr3:119145600-119149600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:119145600-119150200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:119145600-119150200	ZNF genes & repeats	Fetal Kidney	kidney
34	chr3:119145600-119152000	ZNF genes & repeats	Fetal Lung	lung
35	chr3:119145800-119150200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
36	chr3:119145800-119151000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
37	chr3:119145800-119151800	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:119146000-119149400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell

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