Variant report

Variant	rs403093
Chromosome Location	chr18:9553179-9553180
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr18:9553066-9553301	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
PPP4R1	TF binding region

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1617250	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.80[AMR][1000 genomes]
rs167896	0.86[ASN][1000 genomes]
rs179242	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs328994	0.80[ASN][1000 genomes]
rs329009	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs329018	0.84[CEU][hapmap]
rs329021	0.81[AMR][1000 genomes]
rs7239728	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1056407	chr18:9144345-9553764	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv833585	chr18:9401630-9597291	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv3693417	chr18:9512985-9693638	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs403093	RAB31	cis	parietal	SCAN
rs403093	OGT	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9535200-9556800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr18:9544000-9557000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr18:9544000-9570200	Strong transcription	Fetal Intestine Large	intestine
4	chr18:9544000-9575600	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr18:9544200-9553200	Strong transcription	Thymus	Thymus
6	chr18:9544200-9563600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr18:9544400-9553800	Strong transcription	Spleen	Spleen
8	chr18:9544600-9561600	Strong transcription	Stomach Smooth Muscle	stomach
9	chr18:9544600-9563600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr18:9544600-9563600	Strong transcription	Brain Cingulate Gyrus	brain
11	chr18:9544600-9564200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr18:9544600-9564200	Strong transcription	Placenta	Placenta
13	chr18:9544800-9556800	Strong transcription	HMEC	breast
14	chr18:9544800-9557000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr18:9544800-9562000	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr18:9544800-9564600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr18:9544800-9565000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr18:9544800-9572200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr18:9544800-9572400	Strong transcription	Primary T cells from cord blood	blood
20	chr18:9545000-9554200	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr18:9545000-9557000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr18:9545000-9557200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr18:9545000-9562600	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr18:9545000-9563800	Strong transcription	Osteobl	bone
25	chr18:9545000-9564200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr18:9545000-9564200	Strong transcription	Adipose Nuclei	Adipose
27	chr18:9545000-9564400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr18:9545200-9560400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr18:9545200-9561400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr18:9545200-9561600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr18:9545200-9563400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr18:9545200-9572600	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr18:9545400-9560000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr18:9545400-9564000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr18:9545600-9554000	Strong transcription	NHLF	lung
36	chr18:9545800-9556200	Strong transcription	HepG2	liver
37	chr18:9545800-9563600	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr18:9545800-9564200	Strong transcription	Fetal Thymus	thymus
39	chr18:9545800-9565000	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr18:9545800-9570200	Strong transcription	Duodenum Mucosa	Duodenum
41	chr18:9545800-9583600	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr18:9545800-9595200	Strong transcription	Dnd41	blood
43	chr18:9546000-9555200	Strong transcription	Ovary	ovary
44	chr18:9546000-9557200	Strong transcription	NHEK	skin
45	chr18:9546000-9563800	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr18:9546200-9557600	Strong transcription	HUVEC	blood vessel
47	chr18:9546200-9557800	Strong transcription	Brain Substantia Nigra	brain
48	chr18:9546200-9559600	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr18:9546200-9560200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr18:9546200-9564200	Strong transcription	Left Ventricle	heart

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