Variant report

Variant	rs11142179
Chromosome Location	chr9:71035452-71035453
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	chr9:71034332..71036159-chr9:71048559..71051552,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10735596	0.84[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10780922	0.86[TSI][hapmap]
rs10780935	0.86[TSI][hapmap]
rs10868795	0.85[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs10868796	0.82[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10868803	0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs10868804	0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs11142075	0.87[JPT][hapmap]
rs11142199	0.82[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes]
rs11142305	0.81[CHB][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11142334	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11142335	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1492822	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1492823	0.84[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1492824	0.84[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs1887889	0.81[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1976232	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2026033	0.84[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2026034	0.87[CHB][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7020465	0.84[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs7025140	0.85[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11142179	PGM5	cis	multi-tissue	Pritchard

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:70997800-71052600	Weak transcription	HSMMtube	muscle
2	chr9:71027600-71041800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr9:71031000-71035600	Enhancers	Fetal Heart	heart
4	chr9:71032000-71035800	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr9:71032800-71036000	Enhancers	Colon Smooth Muscle	Colon
6	chr9:71033000-71041800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:71033600-71038600	Weak transcription	Aorta	Aorta
8	chr9:71033800-71035800	Enhancers	Stomach Smooth Muscle	stomach
9	chr9:71033800-71040200	Weak transcription	Fetal Lung	lung
10	chr9:71033800-71041600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr9:71033800-71041600	Weak transcription	Fetal Muscle Leg	muscle
12	chr9:71033800-71041800	Weak transcription	Psoas Muscle	Psoas
13	chr9:71035200-71038800	Weak transcription	Right Ventricle	heart
14	chr9:71035200-71040000	Weak transcription	Fetal Stomach	stomach
15	chr9:71035200-71040000	Weak transcription	Right Atrium	heart
16	chr9:71035200-71041600	Weak transcription	Left Ventricle	heart
17	chr9:71035400-71038600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr9:71035400-71041800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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