Variant report

Variant	rs3920702
Chromosome Location	chr9:71170130-71170131
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10120859	0.88[CHB][hapmap]
rs10735603	0.83[ASN][1000 genomes]
rs10746875	0.83[ASN][1000 genomes]
rs10869020	0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs10869034	0.93[ASN][1000 genomes]
rs10869043	0.93[ASN][1000 genomes]
rs11142922	0.84[EUR][1000 genomes]
rs11795256	0.92[ASN][1000 genomes]
rs12340143	0.93[ASN][1000 genomes]
rs12343877	0.92[ASN][1000 genomes]
rs12376362	0.95[ASN][1000 genomes]
rs12685375	0.82[GIH][hapmap]
rs13285683	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1411992	0.96[ASN][1000 genomes]
rs4143073	0.88[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs4457398	0.94[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs4745093	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6560203	0.94[CHB][hapmap]
rs7028200	0.94[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs7036795	0.92[ASN][1000 genomes]
rs7046767	0.92[ASN][1000 genomes]
rs7860486	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs7861495	0.82[CHB][hapmap]

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
rs3920702	PGM5	cis	multi-tissue	Pritchard
rs3920702	PGM5	cis	Whole Blood	GTEx

Chromatin state (count:24 , 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	chr9:71162200-71174800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr9:71162200-71175000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:71163000-71170400	Weak transcription	Fetal Kidney	kidney
5	chr9:71163600-71170400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr9:71166400-71170600	Weak transcription	Primary B cells from cord blood	blood
7	chr9:71166400-71170800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr9:71166600-71173600	Weak transcription	Left Ventricle	heart
9	chr9:71166600-71173600	Weak transcription	Right Atrium	heart
10	chr9:71167400-71170200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr9:71167400-71171200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:71167800-71173000	Weak transcription	Fetal Heart	heart
13	chr9:71168000-71170200	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr9:71168000-71170200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr9:71168000-71173000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr9:71169400-71174400	Weak transcription	Stomach Mucosa	stomach
17	chr9:71169600-71173800	Weak transcription	Colon Smooth Muscle	Colon
18	chr9:71169600-71174800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr9:71169600-71175000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:71169800-71170200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr9:71170000-71170400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:71170000-71170400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:71170000-71170800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
24	chr9:71170000-71175000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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