Variant report

Variant	rs4745375
Chromosome Location	chr9:71513962-71513963
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	chr9:71513862..71516503-chr9:71520061..71522924,2	MCF-7	breast:
2	chr9:71506243..71507747-chr9:71513717..71515425,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10114114	1.00[JPT][hapmap]
rs11143602	1.00[JPT][hapmap]
rs11144206	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12003432	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12005037	0.95[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12344543	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12553327	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12553357	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17059479	1.00[JPT][hapmap]
rs17391162	0.83[MEX][hapmap]
rs17391596	0.83[MEX][hapmap]
rs17391840	0.83[MEX][hapmap]
rs17482181	0.83[MEX][hapmap]
rs17482797	0.83[MEX][hapmap]
rs17483533	0.83[MEX][hapmap]
rs34483859	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4626674	0.83[AMR][1000 genomes]
rs55830509	0.83[AMR][1000 genomes]
rs7018552	1.00[JPT][hapmap];0.87[MEX][hapmap]
rs72720038	0.84[AMR][1000 genomes]
rs73443515	0.81[ASN][1000 genomes]
rs73461629	1.00[ASN][1000 genomes]
rs73461643	1.00[ASN][1000 genomes]
rs883951	0.85[CEU][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS 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	27 gene(s)	inside rSNPs	diseases
8	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv466393	chr9:71453443-71704827	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv614547	chr9:71453443-71704827	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv1035823	chr9:71465139-71901672	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv466396	chr9:71471912-71935577	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
15	nsv614548	chr9:71471912-71935577	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	nsv614549	chr9:71506459-71659280	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv1051798	chr9:71511805-71792032	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
18	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4745375	PGM5	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71459000-71519200	Weak transcription	Colonic Mucosa	Colon
2	chr9:71460800-71517000	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr9:71492400-71515000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:71496600-71515200	Weak transcription	HepG2	liver
5	chr9:71502600-71516600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr9:71508800-71515200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr9:71509200-71514600	Enhancers	Fetal Heart	heart
8	chr9:71509800-71514000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr9:71510400-71514200	Enhancers	Right Ventricle	heart
10	chr9:71510400-71576200	Weak transcription	Stomach Mucosa	stomach
11	chr9:71510600-71515000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:71510600-71532400	Weak transcription	Small Intestine	intestine
13	chr9:71510800-71519800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr9:71511000-71514000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr9:71511000-71514200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:71511200-71514200	Enhancers	Fetal Muscle Leg	muscle
17	chr9:71511200-71514400	Enhancers	Right Atrium	heart
18	chr9:71511200-71519200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr9:71511400-71514200	Enhancers	Left Ventricle	heart
20	chr9:71511600-71514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr9:71511600-71514000	Weak transcription	Brain Hippocampus Middle	brain
22	chr9:71511600-71519800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr9:71511800-71514000	Weak transcription	Ovary	ovary
24	chr9:71511800-71519200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr9:71512000-71514000	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr9:71512000-71514000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr9:71512000-71519800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:71512000-71520000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr9:71512200-71548800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr9:71512400-71517600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr9:71512400-71520200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr9:71512800-71514000	Enhancers	Spleen	Spleen
33	chr9:71512800-71514200	Strong transcription	Fetal Intestine Small	intestine
34	chr9:71512800-71515200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:71512800-71520200	Weak transcription	Primary T cells from cord blood	blood
36	chr9:71512800-71527600	Weak transcription	Pancreas	Pancrea
37	chr9:71513000-71520000	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr9:71513200-71514000	Genic enhancers	Lung	lung
39	chr9:71513400-71516200	Enhancers	GM12878-XiMat	blood
40	chr9:71513600-71514400	Enhancers	Primary B cells from peripheral blood	blood
41	chr9:71513800-71514000	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr9:71513800-71514000	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr9:71513800-71514000	Enhancers	Fetal Stomach	stomach
44	chr9:71513800-71514000	Genic enhancers	Rectal Mucosa Donor 29	rectum
45	chr9:71513800-71514200	Enhancers	Primary B cells from cord blood	blood
46	chr9:71513800-71514200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr9:71513800-71514200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr9:71513800-71514200	Strong transcription	Aorta	Aorta
49	chr9:71513800-71514800	Enhancers	Adipose Nuclei	Adipose
50	chr9:71513800-71517000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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