Variant report

Variant	rs902949
Chromosome Location	chr9:71132918-71132919
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10780985	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1964619	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309312	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs265081	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs372581	1.00[JPT][hapmap]
rs424970	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4406476	1.00[JPT][hapmap]
rs4744621	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56320925	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6560175	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72716013	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7849742	0.95[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7854357	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7862888	0.81[CEU][hapmap]
rs7864227	0.83[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs928049	0.95[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs902949	PGM5	cis	Whole Blood	GTEx
rs902949	PGM5	cis	multi-tissue	Pritchard
rs902949	PGM5	cis	cerebellum	SCAN

Chromatin state (count:17 , 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	chr9:71122200-71133200	Weak transcription	Ovary	ovary
3	chr9:71124800-71133200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr9:71130200-71148000	Weak transcription	HSMMtube	muscle
5	chr9:71130600-71144400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr9:71130600-71144800	Weak transcription	Left Ventricle	heart
7	chr9:71130800-71145400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr9:71131000-71152600	Weak transcription	NHLF	lung
9	chr9:71131400-71136800	Weak transcription	Right Atrium	heart
10	chr9:71131600-71145400	Weak transcription	Right Ventricle	heart
11	chr9:71131800-71133200	ZNF genes & repeats	Fetal Stomach	stomach
12	chr9:71132400-71134000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr9:71132600-71133400	ZNF genes & repeats	Colon Smooth Muscle	Colon
14	chr9:71132800-71133000	ZNF genes & repeats	Stomach Smooth Muscle	stomach
15	chr9:71132800-71133200	ZNF genes & repeats	Aorta	Aorta
16	chr9:71132800-71133600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
17	chr9:71132800-71134000	ZNF genes & repeats	Fetal Lung	lung

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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