Variant report

Variant	rs12343877
Chromosome Location	chr9:71173965-71173966
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10120859	0.83[CHB][hapmap];0.80[CHD][hapmap];0.83[ASN][1000 genomes]
rs10735603	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10746875	0.87[ASN][1000 genomes]
rs10869020	0.83[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap];0.80[YRI][hapmap];0.87[ASN][1000 genomes]
rs10869034	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10869043	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11795256	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12340143	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12376362	0.94[ASN][1000 genomes]
rs13285683	0.91[ASN][1000 genomes]
rs1411992	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs265073	1.00[YRI][hapmap]
rs3920702	0.92[ASN][1000 genomes]
rs404994	0.89[YRI][hapmap]
rs4143073	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4457398	0.86[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4745093	0.94[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs6560203	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs7028200	0.94[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7036795	0.96[ASN][1000 genomes]
rs7046767	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7860486	0.90[CHD][hapmap];0.80[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7861495	0.89[YRI][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12343877	PGM5	cis	multi-tissue	Pritchard

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71162200-71174800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr9:71162200-71175000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr9:71169400-71174400	Weak transcription	Stomach Mucosa	stomach
4	chr9:71169600-71174800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:71169600-71175000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:71170000-71175000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:71170200-71174800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr9:71170400-71175200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr9:71171000-71175000	Weak transcription	Lung	lung
10	chr9:71171200-71174000	Weak transcription	Spleen	Spleen
11	chr9:71171200-71174800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr9:71171200-71175000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:71171200-71175200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:71171400-71174800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:71173000-71176200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr9:71173200-71174600	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr9:71173200-71176200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr9:71173200-71177600	Enhancers	Primary hematopoietic stem cells	blood
19	chr9:71173400-71174200	Weak transcription	Fetal Kidney	kidney
20	chr9:71173400-71175000	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr9:71173400-71175600	Weak transcription	Right Ventricle	heart
22	chr9:71173600-71174600	Weak transcription	Fetal Heart	heart
23	chr9:71173600-71175800	Enhancers	Left Ventricle	heart
24	chr9:71173600-71175800	Enhancers	Right Atrium	heart
25	chr9:71173800-71174400	Enhancers	Primary B cells from cord blood	blood
26	chr9:71173800-71176200	Enhancers	Colon Smooth Muscle	Colon

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