Variant report

Variant	rs9713715
Chromosome Location	chr3:119183704-119183705
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:119181906-119183714	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:119182024..119184224-chr3:119215586..119219856,7	MCF-7	breast:
2	chr3:119181455..119183728-chr3:119216896..119218706,2	MCF-7	breast:
3	chr3:119180899..119185941-chr3:119186195..119190279,17	K562	blood:
4	chr3:119181428..119184178-chr3:119215849..119218868,6	K562	blood:
5	chr3:119181870..119185760-chr3:119214240..119218868,7	K562	blood:
6	chr3:119181316..119183992-chr3:119395288..119397711,2	MCF-7	breast:

No data

Variant related genes	Relation type
POGLUT1	TF binding region
TMEM39A	TF binding region
ENSG00000272662	Chromatin interaction
ENSG00000163389	Chromatin interaction
ENSG00000113845	Chromatin interaction
ENSG00000176142	Chromatin interaction
ENSG00000138495	Chromatin interaction

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	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2049756	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2178318	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2282171	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3195852	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35078244	0.88[EUR][1000 genomes]
rs3772136	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3932422	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687859	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4688003	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6438532	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6763561	0.89[EUR][1000 genomes]
rs6797866	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7613562	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7629750	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9846088	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851177	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855347	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9872589	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[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	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9713715	POGLUT1	cis	Artery Tibial	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119183000-119187000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:119183000-119187200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:119183000-119187200	Weak transcription	Right Atrium	heart
4	chr3:119183000-119187400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:119183000-119187400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:119183000-119187400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:119183000-119187400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:119183000-119187400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:119183000-119187400	Weak transcription	Gastric	stomach
10	chr3:119183000-119187400	Weak transcription	Ovary	ovary
11	chr3:119183000-119187400	Weak transcription	Small Intestine	intestine
12	chr3:119183200-119184000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:119183200-119186800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:119183200-119186800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr3:119183200-119186800	Weak transcription	Primary B cells from peripheral blood	blood
16	chr3:119183200-119186800	Weak transcription	Brain Substantia Nigra	brain
17	chr3:119183200-119186800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:119183200-119186800	Weak transcription	Fetal Brain Male	brain
19	chr3:119183200-119186800	Weak transcription	Right Ventricle	heart
20	chr3:119183200-119186800	Weak transcription	Hela-S3	cervix
21	chr3:119183200-119187000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:119183200-119187000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:119183200-119187000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:119183200-119187000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:119183200-119187000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:119183200-119187000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:119183200-119187000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:119183200-119187000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:119183200-119187000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:119183200-119187000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:119183200-119187000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:119183200-119187000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:119183200-119187000	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr3:119183200-119187000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr3:119183200-119187000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr3:119183200-119187000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:119183200-119187000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:119183200-119187000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:119183200-119187000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:119183200-119187000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:119183200-119187000	Weak transcription	Adipose Nuclei	Adipose
42	chr3:119183200-119187000	Weak transcription	Liver	Liver
43	chr3:119183200-119187000	Weak transcription	Brain Anterior Caudate	brain
44	chr3:119183200-119187000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr3:119183200-119187000	Weak transcription	Colon Smooth Muscle	Colon
46	chr3:119183200-119187000	Weak transcription	Fetal Heart	heart
47	chr3:119183200-119187000	Weak transcription	Fetal Intestine Large	intestine
48	chr3:119183200-119187000	Weak transcription	Fetal Intestine Small	intestine
49	chr3:119183200-119187000	Weak transcription	Fetal Lung	lung
50	chr3:119183200-119187000	Weak transcription	Rectal Smooth Muscle	rectum

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