Variant report

Variant	rs530978
Chromosome Location	chr9:79324179-79324180
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	chr9:79073827..79075700-chr9:79322081..79324440,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187210	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10512061	0.90[JPT][hapmap]
rs10735649	0.90[JPT][hapmap]
rs1536820	0.90[JPT][hapmap]
rs2487263	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs471083	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs488165	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs489069	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs491798	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs498266	0.83[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap]
rs506965	0.89[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap]
rs511545	0.91[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap]
rs519983	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]
rs520365	0.83[CEU][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap];0.81[TSI][hapmap]
rs537903	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs551262	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs557352	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs571960	1.00[ASW][hapmap];0.96[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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs577993	0.83[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs579025	0.83[CEU][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap]
rs600859	0.87[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs620985	0.93[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs626837	0.92[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs630423	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs641088	0.92[CEU][hapmap];0.85[CHB][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs658548	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]
rs659003	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs677061	0.80[JPT][hapmap]
rs683866	0.87[CEU][hapmap];0.83[CHB][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs684639	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs685011	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs700757	0.90[JPT][hapmap];0.81[YRI][hapmap]

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
rs530978	PRUNE2	cis	cerebellum	SCAN
rs530978	TLE4	cis	parietal	SCAN
rs530978	VPS13A	cis	parietal	SCAN
rs530978	PRUNE2	cis	Whole Blood	GTEx

Chromatin state (count:30 , 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	chr9:79316800-79325400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr9:79316800-79331000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr9:79316800-79331200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr9:79317400-79327800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr9:79317400-79328600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr9:79317600-79330800	Strong transcription	HSMM	muscle
12	chr9:79317800-79328600	Strong transcription	HSMMtube	muscle
13	chr9:79318000-79330400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr9:79318400-79330000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr9:79320000-79328000	Strong transcription	Aorta	Aorta
16	chr9:79320000-79328800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:79320000-79331200	Weak transcription	Brain Anterior Caudate	brain
18	chr9:79320000-79332000	Weak transcription	Brain Angular Gyrus	brain
19	chr9:79320400-79328600	Strong transcription	Stomach Smooth Muscle	stomach
20	chr9:79321800-79324600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:79322000-79324600	Weak transcription	Colonic Mucosa	Colon
22	chr9:79322200-79324200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr9:79322400-79327000	Strong transcription	Colon Smooth Muscle	Colon
24	chr9:79322800-79324800	Strong transcription	Brain Cingulate Gyrus	brain
25	chr9:79322800-79326000	Strong transcription	Brain Hippocampus Middle	brain
26	chr9:79323200-79324800	Strong transcription	Brain Substantia Nigra	brain
27	chr9:79323600-79324600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:79324000-79324800	Weak transcription	Fetal Stomach	stomach
29	chr9:79324000-79326800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr9:79324000-79332200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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