Variant report

Variant	rs9872589
Chromosome Location	chr3:119151227-119151228
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119139525..119141097-chr3:119150989..119153338,2	K562	blood:
2	chr3:119145344..119146916-chr3:119149020..119151478,2	MCF-7	breast:
3	chr3:119150195..119152799-chr3:119173269..119174905,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

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	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];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	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs3932422	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4687859	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4688003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438532	0.95[CEU][hapmap];0.81[JPT][hapmap];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]
rs7430156	0.81[MKK][hapmap]
rs7613562	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7629750	0.94[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];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	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];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]

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
rs9872589	POGLUT1	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119138000-119152400	Weak transcription	Lung	lung
2	chr3:119144600-119152000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:119145600-119152000	ZNF genes & repeats	Fetal Lung	lung
4	chr3:119145800-119151800	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:119147000-119151800	Strong transcription	NH-A	brain
6	chr3:119147000-119152800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:119147000-119179000	Strong transcription	Osteobl	bone
8	chr3:119147200-119152200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
9	chr3:119147200-119180400	Weak transcription	Stomach Mucosa	stomach
10	chr3:119147400-119152800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:119147400-119157200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:119147400-119179200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:119147600-119157200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:119147600-119157400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:119147600-119157400	Strong transcription	Fetal Thymus	thymus
16	chr3:119147800-119154400	Strong transcription	K562	blood
17	chr3:119147800-119157000	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr3:119147800-119157000	Strong transcription	Placenta Amnion	Placenta Amnion
19	chr3:119147800-119157200	Strong transcription	Rectal Smooth Muscle	rectum
20	chr3:119147800-119157400	Strong transcription	Placenta	Placenta
21	chr3:119147800-119157400	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:119147800-119157600	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr3:119147800-119157600	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr3:119147800-119159400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:119148000-119157000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr3:119148000-119157000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:119148000-119157000	Strong transcription	Brain Cingulate Gyrus	brain
28	chr3:119148000-119162200	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:119148200-119151800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:119148200-119151800	Strong transcription	Adipose Nuclei	Adipose
31	chr3:119148200-119157000	Strong transcription	NHLF	lung
32	chr3:119148200-119157200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:119148200-119157200	Strong transcription	Brain Hippocampus Middle	brain
34	chr3:119148400-119153200	Strong transcription	Fetal Stomach	stomach
35	chr3:119148400-119156800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr3:119148400-119157000	Strong transcription	Fetal Muscle Trunk	muscle
37	chr3:119148400-119157200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
38	chr3:119148400-119157200	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr3:119148400-119157400	Strong transcription	NHDF-Ad	bronchial
40	chr3:119148400-119157600	Strong transcription	HepG2	liver
41	chr3:119148600-119157200	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr3:119148600-119157200	Strong transcription	Brain Substantia Nigra	brain
43	chr3:119148800-119151400	Strong transcription	Thymus	Thymus
44	chr3:119148800-119156800	Weak transcription	Right Atrium	heart
45	chr3:119148800-119157000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr3:119148800-119157200	Strong transcription	Primary B cells from peripheral blood	blood
47	chr3:119148800-119157800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr3:119148800-119157800	Strong transcription	Stomach Smooth Muscle	stomach
49	chr3:119148800-119175400	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr3:119148800-119180400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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