Variant report

Variant	rs11145045
Chromosome Location	chr9:79367367-79367368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10119901	0.80[ASN][1000 genomes]
rs10735649	0.94[CHB][hapmap]
rs10781378	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10869809	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10869814	0.80[ASN][1000 genomes]
rs17784809	0.84[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs512781	0.80[ASN][1000 genomes]
rs514673	0.80[ASN][1000 genomes]
rs515381	0.80[ASN][1000 genomes]
rs536897	0.80[ASN][1000 genomes]
rs577144	0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs615037	0.80[ASN][1000 genomes]
rs627176	0.80[ASN][1000 genomes]
rs627587	0.80[ASN][1000 genomes]
rs629806	0.80[ASN][1000 genomes]
rs670879	0.89[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs673575	0.81[ASN][1000 genomes]
rs7022379	0.80[ASN][1000 genomes]
rs7025345	0.80[ASN][1000 genomes]
rs7035263	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7037399	0.80[ASN][1000 genomes]
rs7037532	0.80[ASN][1000 genomes]
rs7040264	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7859406	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7860042	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7868392	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv2758190	chr9:79365865-79673907	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2759697	chr9:79365865-79673907	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11145045	TAB2	trans	cerebellum	SCAN
rs11145045	CENPJ	trans	parietal	SCAN
rs11145045	C9orf85	cis	parietal	SCAN
rs11145045	GCNT1	cis	parietal	SCAN
rs11145045	PRUNE2	cis	Whole Blood	GTEx
rs11145045	PRUNE2	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79333200-79370000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr9:79348200-79370200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:79348400-79370200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr9:79348400-79370200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr9:79358400-79370800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr9:79361200-79396600	Weak transcription	Aorta	Aorta
7	chr9:79362200-79370400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:79364400-79372000	Weak transcription	Brain Hippocampus Middle	brain
9	chr9:79364600-79371200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr9:79364600-79371200	Weak transcription	Brain Substantia Nigra	brain
11	chr9:79364600-79371400	Weak transcription	Brain Angular Gyrus	brain
12	chr9:79364600-79387000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr9:79364800-79370600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr9:79364800-79373600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr9:79364800-79374800	Weak transcription	Colon Smooth Muscle	Colon
16	chr9:79366000-79370200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:79366000-79370400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr9:79366000-79371200	Weak transcription	Fetal Muscle Leg	muscle
19	chr9:79366200-79368800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr9:79366200-79370000	Weak transcription	HSMM	muscle
21	chr9:79366600-79370000	Weak transcription	HSMMtube	muscle
22	chr9:79367000-79370200	Weak transcription	Primary B cells from cord blood	blood

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