Variant report

Variant	rs10869800
Chromosome Location	chr9:79330946-79330947
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10781370	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10781371	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10869797	0.81[EUR][1000 genomes]
rs10869798	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10869805	0.87[ASN][1000 genomes]
rs11145011	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11145012	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11145017	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11145018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11145019	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11145021	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11145023	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12238013	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12683741	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1329014	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2077181	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2277155	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3739521	1.00[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3739524	0.92[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs537903	0.83[ASN][1000 genomes]
rs57608282	0.87[ASN][1000 genomes]
rs577993	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs600859	0.83[ASN][1000 genomes]
rs626837	0.80[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs641088	0.81[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs658548	0.81[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs683866	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs7042953	0.87[ASN][1000 genomes]
rs9314853	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9785303	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10869800	PRUNE2	cis	cerebellum	SCAN

Chromatin state (count:31 , 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	chr9:79316400-79332000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:79316800-79331000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr9:79316800-79331200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:79320000-79331200	Weak transcription	Brain Anterior Caudate	brain
6	chr9:79320000-79332000	Weak transcription	Brain Angular Gyrus	brain
7	chr9:79324000-79332200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:79324800-79331000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:79326200-79332000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr9:79326200-79332000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr9:79326400-79331000	Weak transcription	Brain Substantia Nigra	brain
12	chr9:79327000-79331000	Weak transcription	Colon Smooth Muscle	Colon
13	chr9:79327800-79332000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr9:79327800-79341800	Weak transcription	Fetal Stomach	stomach
15	chr9:79328000-79331000	Weak transcription	Fetal Intestine Small	intestine
16	chr9:79328000-79341200	Weak transcription	Aorta	Aorta
17	chr9:79328200-79332000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr9:79328600-79331200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:79328600-79331200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:79328600-79332000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr9:79328600-79332600	Weak transcription	Fetal Muscle Leg	muscle
22	chr9:79328800-79331000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr9:79329200-79333200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr9:79329600-79331200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr9:79330000-79331000	Weak transcription	HSMMtube	muscle
26	chr9:79330400-79333600	Enhancers	Rectal Smooth Muscle	rectum
27	chr9:79330400-79334000	Enhancers	Brain Hippocampus Middle	brain
28	chr9:79330800-79331200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:79330800-79331200	Weak transcription	HSMM	muscle
30	chr9:79330800-79333400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr9:79330800-79333400	Enhancers	HUVEC	blood vessel

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