Variant report

Variant	rs13285683
Chromosome Location	chr9:71167741-71167742
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:71162331..71165106-chr9:71166259..71168018,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10120859	0.81[CHB][hapmap]
rs10735603	0.82[ASN][1000 genomes]
rs10746875	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs10869020	0.81[CHB][hapmap];0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs10869034	0.92[ASN][1000 genomes]
rs10869043	0.92[ASN][1000 genomes]
rs11142922	0.83[EUR][1000 genomes]
rs11795256	0.93[ASN][1000 genomes]
rs12340143	0.92[ASN][1000 genomes]
rs12343877	0.91[ASN][1000 genomes]
rs12376362	0.94[ASN][1000 genomes]
rs12685375	0.82[GIH][hapmap]
rs1411992	0.95[ASN][1000 genomes]
rs3920702	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4143073	0.94[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs4457398	0.88[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs4745093	0.81[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6560203	0.88[CHB][hapmap];0.81[CHD][hapmap]
rs7028200	0.87[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs7036795	0.93[ASN][1000 genomes]
rs7046767	0.92[ASN][1000 genomes]
rs7860486	0.88[CHB][hapmap];0.84[CHD][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893413	chr9:71130848-71196984	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv893411	chr9:71130848-71199545	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv893412	chr9:71130848-71199545	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1024967	chr9:71130848-71210031	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv482506	chr9:71130848-71280888	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv466392	chr9:71130848-71318817	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv614546	chr9:71130848-71318817	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1026962	chr9:71130848-71357605	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv893414	chr9:71139378-71320732	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13285683	PGM5	cis	Whole Blood	GTEx
rs13285683	PGM5	cis	multi-tissue	Pritchard

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71152200-71170600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:71162000-71167800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr9:71162000-71169800	Weak transcription	Gastric	stomach
4	chr9:71162200-71174800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr9:71162200-71175000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr9:71163000-71170400	Weak transcription	Fetal Kidney	kidney
7	chr9:71163200-71168000	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr9:71163600-71170400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr9:71165400-71167800	Enhancers	Fetal Intestine Large	intestine
10	chr9:71165400-71168000	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr9:71165600-71169400	Enhancers	Stomach Mucosa	stomach
12	chr9:71166000-71168000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr9:71166000-71169600	Enhancers	Colon Smooth Muscle	Colon
14	chr9:71166000-71169600	Enhancers	Rectal Smooth Muscle	rectum
15	chr9:71166400-71170600	Weak transcription	Primary B cells from cord blood	blood
16	chr9:71166400-71170800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr9:71166600-71173600	Weak transcription	Left Ventricle	heart
18	chr9:71166600-71173600	Weak transcription	Right Atrium	heart
19	chr9:71166800-71168000	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr9:71166800-71170000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr9:71167000-71167800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr9:71167000-71168000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:71167000-71168200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:71167200-71168600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:71167400-71168200	Enhancers	Muscle Satellite Cultured Cells	--
26	chr9:71167400-71168600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:71167400-71168600	Enhancers	NHDF-Ad	bronchial
28	chr9:71167400-71168800	Enhancers	NHLF	lung
29	chr9:71167400-71170200	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr9:71167400-71171200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:71167600-71167800	Enhancers	Fetal Heart	heart
32	chr9:71167600-71167800	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr9:71167600-71168000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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