Variant report

Variant	rs658548
Chromosome Location	chr9:79329257-79329258
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10781370	0.83[ASN][1000 genomes]
rs10781371	0.83[ASN][1000 genomes]
rs10869800	0.83[ASN][1000 genomes]
rs11145011	0.80[ASN][1000 genomes]
rs11145012	0.81[ASN][1000 genomes]
rs11145017	0.81[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs11145018	0.81[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs11145019	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs11145021	0.81[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs12238013	0.81[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1329014	0.83[ASN][1000 genomes]
rs2077181	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2277155	0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2487263	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3739521	0.81[JPT][hapmap]
rs3739524	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs471083	0.84[AMR][1000 genomes]
rs488165	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs489069	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs491798	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs506965	0.82[MEX][hapmap]
rs511545	0.95[MEX][hapmap]
rs519983	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs530978	0.81[ASW][hapmap];0.87[CEU][hapmap];0.85[CHB][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs537903	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551262	0.87[CEU][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs557352	0.87[CEU][hapmap];0.90[CHB][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs571960	0.81[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs577993	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs600859	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620985	0.92[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs626837	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs630423	0.87[CEU][hapmap];0.90[CHB][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs641088	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659003	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs683866	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs684639	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs685011	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9785303	0.81[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	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
4	nsv893481	chr9:79304043-79348193	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv2754389	chr9:79318677-79333056	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs658548	PRUNE2	cis	cerebellum	SCAN
rs658548	TLE4	cis	parietal	SCAN
rs658548	PRUNE2	cis	Whole Blood	GTEx
rs658548	VPS13A	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79300400-79332200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:79316200-79330800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr9:79316400-79332000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr9:79316800-79331000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr9:79316800-79331200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:79317600-79330800	Strong transcription	HSMM	muscle
7	chr9:79318000-79330400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr9:79318400-79330000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:79320000-79331200	Weak transcription	Brain Anterior Caudate	brain
10	chr9:79320000-79332000	Weak transcription	Brain Angular Gyrus	brain
11	chr9:79324000-79332200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:79324800-79331000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr9:79326000-79330400	Weak transcription	Brain Hippocampus Middle	brain
14	chr9:79326200-79332000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr9:79326200-79332000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr9:79326400-79331000	Weak transcription	Brain Substantia Nigra	brain
17	chr9:79327000-79331000	Weak transcription	Colon Smooth Muscle	Colon
18	chr9:79327800-79332000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:79327800-79341800	Weak transcription	Fetal Stomach	stomach
20	chr9:79328000-79331000	Weak transcription	Fetal Intestine Small	intestine
21	chr9:79328000-79341200	Weak transcription	Aorta	Aorta
22	chr9:79328200-79329600	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr9:79328200-79330400	Enhancers	HUVEC	blood vessel
24	chr9:79328200-79332000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr9:79328600-79329800	Weak transcription	HSMMtube	muscle
26	chr9:79328600-79330800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:79328600-79331200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:79328600-79331200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr9:79328600-79332000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr9:79328600-79332600	Weak transcription	Fetal Muscle Leg	muscle
31	chr9:79328800-79329400	Weak transcription	Left Ventricle	heart
32	chr9:79328800-79331000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:79329200-79329800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
34	chr9:79329200-79333200	Enhancers	Cortex derived primary cultured neurospheres	brain

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