Variant report

Variant	rs519983
Chromosome Location	chr9:79313525-79313526
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:79307128..79309630-chr9:79312231..79313981,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10512061	0.90[JPT][hapmap]
rs10735649	0.90[JPT][hapmap]
rs10869797	0.81[ASN][1000 genomes]
rs11145009	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1536820	0.90[JPT][hapmap]
rs2487263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471083	0.88[ASN][1000 genomes]
rs488165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489069	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491798	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs498266	0.83[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs506965	0.88[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs511545	0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs520365	0.83[CEU][hapmap];0.80[JPT][hapmap]
rs530978	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs537903	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs551262	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs557352	1.00[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs571960	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs577993	0.87[CEU][hapmap]
rs579025	0.83[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs600859	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs620985	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs625426	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs626837	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs630423	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs641088	0.96[CEU][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs658548	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs659003	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs677061	0.80[CEU][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs683866	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs684639	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs685011	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs700757	0.84[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs519983	PRUNE2	cis	Whole Blood	GTEx

Chromatin state (count:28 , 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	chr9:79307400-79315800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr9:79307400-79317600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:79307600-79314400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:79307600-79314600	Weak transcription	Colon Smooth Muscle	Colon
6	chr9:79307600-79315800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr9:79307800-79314400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr9:79307800-79314800	Weak transcription	Fetal Brain Female	brain
9	chr9:79307800-79316000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:79308000-79314400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:79308000-79315800	Weak transcription	Aorta	Aorta
12	chr9:79308000-79315800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr9:79308400-79314800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr9:79308400-79314800	Weak transcription	Brain Hippocampus Middle	brain
15	chr9:79309000-79314400	Weak transcription	Fetal Muscle Leg	muscle
16	chr9:79309000-79314400	Weak transcription	Fetal Thymus	thymus
17	chr9:79309200-79315600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr9:79312000-79316600	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr9:79312200-79315000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr9:79312600-79314200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:79312600-79314800	Weak transcription	Brain Angular Gyrus	brain
22	chr9:79312800-79314200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:79312800-79314200	Weak transcription	HSMM	muscle
24	chr9:79312800-79314400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:79313000-79314400	Weak transcription	HSMMtube	muscle
26	chr9:79313000-79316000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr9:79313200-79315200	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr9:79313400-79315000	Weak transcription	Stomach Mucosa	stomach

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