Variant report

Variant	rs4744683
Chromosome Location	chr9:71325181-71325182
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71324675..71326449-chr9:71333129..71335717,2	K562	blood:
2	chr9:71320129..71321713-chr9:71324484..71326376,3	K562	blood:
3	chr9:71320513..71323388-chr9:71323733..71326341,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000107242	Chromatin interaction

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

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

rs_ID	r²[population]
rs10121993	0.83[CHB][hapmap];0.93[CHD][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs10217316	0.83[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs10746919	0.84[ASN][1000 genomes]
rs10781117	0.89[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs10781119	0.84[ASN][1000 genomes]
rs10869225	0.89[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs10869245	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2151412	0.88[ASN][1000 genomes]
rs2151416	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2151417	0.89[ASN][1000 genomes]
rs2151418	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2184117	0.83[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4352908	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4534183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744680	0.89[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs4744685	0.83[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4745223	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4745227	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]
rs4745228	0.89[CHB][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap]
rs4745229	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4745230	0.83[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs6560316	0.89[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.80[ASN][1000 genomes]
rs7021661	0.84[ASN][1000 genomes]
rs7853748	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7857057	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7867941	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	esv2752385	chr9:71304465-71332240	Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	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
rs4744683	PGM5	cis	multi-tissue	Pritchard

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71321800-71329200	Weak transcription	Gastric	stomach
2	chr9:71321800-71329400	Weak transcription	Lung	lung
3	chr9:71322000-71329800	Weak transcription	Pancreas	Pancrea
4	chr9:71322000-71349400	Weak transcription	Aorta	Aorta
5	chr9:71322200-71329400	Weak transcription	Left Ventricle	heart
6	chr9:71322200-71335000	Weak transcription	Placenta	Placenta
7	chr9:71322400-71325800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr9:71322600-71327400	Enhancers	HepG2	liver
9	chr9:71322600-71329600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr9:71322600-71329800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr9:71322800-71325200	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr9:71322800-71326200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr9:71322800-71326800	Weak transcription	Right Ventricle	heart
14	chr9:71322800-71333400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr9:71323000-71326200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:71323400-71326200	Enhancers	Duodenum Mucosa	Duodenum
17	chr9:71323400-71331800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr9:71323600-71335800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr9:71324000-71329200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr9:71324200-71325200	Genic enhancers	Primary B cells from cord blood	blood
21	chr9:71324200-71326200	Enhancers	Stomach Mucosa	stomach
22	chr9:71324400-71325200	Genic enhancers	Primary B cells from peripheral blood	blood
23	chr9:71324400-71325800	Enhancers	Primary hematopoietic stem cells	blood
24	chr9:71324400-71329400	Weak transcription	Colonic Mucosa	Colon
25	chr9:71324400-71346400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr9:71324600-71325200	Genic enhancers	K562	blood
27	chr9:71324600-71326200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:71324600-71329200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr9:71324800-71325200	Flanking Active TSS	GM12878-XiMat	blood
30	chr9:71324800-71325800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr9:71324800-71325800	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr9:71324800-71326200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr9:71324800-71326400	Enhancers	Brain Germinal Matrix	brain
34	chr9:71325000-71325200	Flanking Active TSS	Fetal Heart	heart
35	chr9:71325000-71325600	Active TSS	Right Atrium	heart
36	chr9:71325000-71326200	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr9:71325000-71326800	Enhancers	Fetal Intestine Small	intestine
38	chr9:71325000-71327600	Enhancers	Fetal Intestine Large	intestine

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