Variant report

Variant	rs4745227
Chromosome Location	chr9:71344278-71344279
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10121993	0.89[CHB][hapmap];0.93[CHD][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs10217316	0.89[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs10746919	0.85[ASN][1000 genomes]
rs10781117	0.84[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs10781119	0.84[ASN][1000 genomes]
rs10869225	0.84[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.84[ASN][1000 genomes]
rs10869245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2151412	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2151416	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2151417	0.86[ASN][1000 genomes]
rs2151418	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2184117	0.89[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs4352908	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4534183	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744680	0.84[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs4744683	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744685	0.89[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs4745223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4745228	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs4745229	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4745230	0.89[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs6560316	0.84[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs7021661	0.85[ASN][1000 genomes]
rs7853748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7857057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7867941	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS 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
4	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	esv2757339	chr9:71291107-71353743	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2759693	chr9:71291107-71353743	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4745227	PGM5	cis	multi-tissue	Pritchard

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71322000-71349400	Weak transcription	Aorta	Aorta
2	chr9:71324400-71346400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:71334000-71345600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:71335000-71345000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr9:71335200-71346200	Weak transcription	Small Intestine	intestine
6	chr9:71336600-71346400	Weak transcription	Left Ventricle	heart
7	chr9:71337000-71350600	Weak transcription	Gastric	stomach
8	chr9:71342600-71344600	Strong transcription	Primary hematopoietic stem cells	blood
9	chr9:71342600-71345800	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr9:71342600-71347400	Strong transcription	Primary B cells from cord blood	blood
11	chr9:71342600-71354600	Enhancers	Fetal Intestine Large	intestine
12	chr9:71343000-71346000	Weak transcription	K562	blood
13	chr9:71343200-71344400	Enhancers	Fetal Intestine Small	intestine
14	chr9:71343400-71346000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr9:71343400-71363000	Weak transcription	GM12878-XiMat	blood
16	chr9:71343600-71344600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr9:71343600-71346000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr9:71343800-71344800	Weak transcription	Stomach Mucosa	stomach
19	chr9:71343800-71345600	Weak transcription	Fetal Heart	heart
20	chr9:71343800-71346200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:71343800-71347800	Weak transcription	Right Atrium	heart
22	chr9:71343800-71357200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr9:71344000-71344400	Weak transcription	HepG2	liver

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