Variant report

Variant	rs12552415
Chromosome Location	chr9:71141490-71141491
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:71140302..71143240-chr9:71143609..71146206,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10120745	1.00[YRI][hapmap]
rs10123848	1.00[YRI][hapmap]
rs11142713	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1158127	0.89[ASW][hapmap]
rs12341862	1.00[YRI][hapmap]
rs12348463	1.00[YRI][hapmap]
rs12351373	1.00[YRI][hapmap]
rs2860101	1.00[JPT][hapmap]
rs398222	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs41305537	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41312182	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714401	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72716004	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427847	chr9:70318730-71153527	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
rs12552415	PGM5	cis	multi-tissue	Pritchard

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71117600-71142800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr9:71130200-71148000	Weak transcription	HSMMtube	muscle
3	chr9:71130600-71144400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:71130600-71144800	Weak transcription	Left Ventricle	heart
5	chr9:71130800-71145400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr9:71131000-71152600	Weak transcription	NHLF	lung
7	chr9:71131600-71145400	Weak transcription	Right Ventricle	heart
8	chr9:71133200-71145400	Weak transcription	Fetal Intestine Small	intestine
9	chr9:71133200-71145600	Weak transcription	Aorta	Aorta
10	chr9:71133400-71143400	Weak transcription	Colon Smooth Muscle	Colon
11	chr9:71134000-71144200	Weak transcription	Fetal Lung	lung
12	chr9:71137000-71144800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr9:71137600-71144200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr9:71137600-71156000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr9:71137800-71145400	Weak transcription	Fetal Heart	heart
16	chr9:71138000-71143800	Weak transcription	Fetal Muscle Leg	muscle
17	chr9:71138200-71143200	Weak transcription	Right Atrium	heart
18	chr9:71138200-71145600	Weak transcription	Gastric	stomach
19	chr9:71138200-71146000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr9:71138200-71146600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr9:71138400-71144800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr9:71138400-71148400	Weak transcription	Esophagus	oesophagus
23	chr9:71138600-71145400	Weak transcription	Fetal Kidney	kidney
24	chr9:71138800-71143600	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr9:71139400-71145600	Weak transcription	Placenta	Placenta
26	chr9:71139600-71161600	Weak transcription	Spleen	Spleen
27	chr9:71140000-71145600	Weak transcription	Ovary	ovary
28	chr9:71140400-71141800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr9:71140400-71144200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr9:71141400-71143800	Weak transcription	Fetal Stomach	stomach
31	chr9:71141400-71151800	Weak transcription	Fetal Muscle Trunk	muscle

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