Variant report

Variant	rs506965
Chromosome Location	chr9:79310655-79310656
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:79074075..79075836-chr9:79309039..79310925,2	MCF-7	breast:
2	chr9:79305411..79307396-chr9:79308812..79311308,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106772	Chromatin interaction
ENSG00000187210	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10512061	0.90[JPT][hapmap]
rs11145009	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1536820	0.90[JPT][hapmap]
rs2487263	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2553212	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2553213	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs488165	0.88[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs489069	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs498266	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs511545	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs519983	0.88[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs520365	0.92[CEU][hapmap];0.84[CHB][hapmap];0.80[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs530978	0.89[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap]
rs551262	0.83[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs557352	0.85[GIH][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap]
rs571960	0.89[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap]
rs579025	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs620985	0.89[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap]
rs625426	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs630423	0.90[JPT][hapmap]
rs658548	0.82[MEX][hapmap]
rs677061	0.87[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs683866	0.82[MEX][hapmap]
rs684639	0.81[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs685011	0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs700757	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs786597	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[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	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs506965	PRUNE2	cis	Whole Blood	GTEx
rs506965	TLE4	cis	parietal	SCAN
rs506965	PRUNE2	cis	cerebellum	SCAN
rs506965	VPS13A	cis	parietal	SCAN
rs506965	TMC1	cis	parietal	SCAN
rs506965	KIAA0367	cis	multi-tissue	Pritchard

Chromatin state (count:26 , 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	chr9:79307600-79312000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr9:79307600-79312200	Weak transcription	HSMMtube	muscle
6	chr9:79307600-79312400	Weak transcription	Stomach Mucosa	stomach
7	chr9:79307600-79314400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:79307600-79314600	Weak transcription	Colon Smooth Muscle	Colon
9	chr9:79307600-79315800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr9:79307800-79312400	Weak transcription	HSMM	muscle
11	chr9:79307800-79314400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:79307800-79314800	Weak transcription	Fetal Brain Female	brain
13	chr9:79307800-79316000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:79308000-79314400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:79308000-79315800	Weak transcription	Aorta	Aorta
16	chr9:79308000-79315800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr9:79308400-79314800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:79308400-79314800	Weak transcription	Brain Hippocampus Middle	brain
19	chr9:79309000-79314400	Weak transcription	Fetal Muscle Leg	muscle
20	chr9:79309000-79314400	Weak transcription	Fetal Thymus	thymus
21	chr9:79309200-79315600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr9:79309600-79312200	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr9:79309600-79312600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr9:79309600-79312800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:79309800-79312000	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr9:79310400-79313000	Strong transcription	Stomach Smooth Muscle	stomach

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