Variant report

Variant	rs577993
Chromosome Location	chr9:79321871-79321872
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:79077933..79079433-chr9:79321608..79323340,2	K562	blood:
2	chr9:79213561..79216371-chr9:79320656..79323527,2	MCF-7	breast:
3	chr9:79321119..79322904-chr9:79325137..79328012,2	MCF-7	breast:
4	chr9:79296367..79298472-chr9:79320957..79323696,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106772	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10781370	0.82[ASN][1000 genomes]
rs10781371	0.82[ASN][1000 genomes]
rs10869800	0.82[ASN][1000 genomes]
rs11145011	0.80[ASN][1000 genomes]
rs11145012	0.81[ASN][1000 genomes]
rs11145017	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs11145018	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs11145019	0.80[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11145021	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs12238013	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1329014	0.82[ASN][1000 genomes]
rs2077181	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2277155	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs3739521	0.81[JPT][hapmap]
rs3739524	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs471083	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs488165	0.83[CEU][hapmap]
rs491798	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs511545	0.91[MEX][hapmap]
rs519983	0.87[CEU][hapmap]
rs530978	0.83[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs537903	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs551262	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs557352	0.83[CEU][hapmap];0.84[CHB][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs571960	0.88[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs600859	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs620985	0.88[CEU][hapmap];0.84[CHB][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs626837	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs630423	0.83[CEU][hapmap];0.84[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs641088	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs658548	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]
rs659003	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs683866	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs684639	0.83[CEU][hapmap]
rs685011	0.83[CEU][hapmap]
rs9785303	0.91[JPT][hapmap];0.82[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs577993	PRUNE2	cis	cerebellum	SCAN
rs577993	PRUNE2	cis	Whole Blood	GTEx
rs577993	KIAA0367	cis	multi-tissue	Pritchard

Chromatin state (count:25 , 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	chr9:79315200-79327600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:79316200-79330800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr9:79316400-79332000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:79316600-79324600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr9:79316800-79322800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr9:79316800-79325400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr9:79316800-79331000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr9:79316800-79331200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:79317400-79327800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:79317400-79328600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:79317600-79330800	Strong transcription	HSMM	muscle
13	chr9:79317800-79328600	Strong transcription	HSMMtube	muscle
14	chr9:79318000-79330400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr9:79318400-79330000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:79318800-79323200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:79320000-79322800	Weak transcription	Brain Hippocampus Middle	brain
18	chr9:79320000-79328000	Strong transcription	Aorta	Aorta
19	chr9:79320000-79328800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:79320000-79331200	Weak transcription	Brain Anterior Caudate	brain
21	chr9:79320000-79332000	Weak transcription	Brain Angular Gyrus	brain
22	chr9:79320200-79322400	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:79320200-79323200	Weak transcription	Brain Substantia Nigra	brain
24	chr9:79320400-79328600	Strong transcription	Stomach Smooth Muscle	stomach
25	chr9:79321800-79324600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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