Variant report

Variant	rs1547559
Chromosome Location	chr8:8499128-8499129
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:8458349..8461087-chr8:8498187..8500312,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10085952	0.81[ASN][1000 genomes]
rs10086172	0.91[ASN][1000 genomes]
rs10089557	0.86[ASN][1000 genomes]
rs10101173	0.91[ASN][1000 genomes]
rs10102100	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10108056	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs12541510	0.91[ASN][1000 genomes]
rs12675028	0.91[ASN][1000 genomes]
rs12675306	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1972312	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2409046	0.90[ASN][1000 genomes]
rs2409048	0.92[ASN][1000 genomes]
rs28541872	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4449799	0.91[ASN][1000 genomes]
rs4841005	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4841006	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs57249973	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61040371	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6981638	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6986287	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6996523	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7007564	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7834476	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs940028	0.97[ASN][1000 genomes]
rs940029	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1025994	chr8:8108863-8580201	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1030433	chr8:8130629-8653691	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv539447	chr8:8130629-8653691	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv1033463	chr8:8221922-8674333	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv539451	chr8:8221922-8674333	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv1019613	chr8:8239352-8636357	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv539452	chr8:8239352-8636357	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv1019606	chr8:8353661-8736992	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv539456	chr8:8353661-8736992	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv995047	chr8:8353662-8857913	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv890336	chr8:8396676-8500562	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1016933	chr8:8432279-8624770	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv610179	chr8:8471348-8501322	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv1022511	chr8:8493992-8737132	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
16	nsv539457	chr8:8493992-8737132	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1547559	PPP1R3B	cis	parietal	SCAN
rs1547559	PPP1R3B	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8489200-8513000	Weak transcription	Gastric	stomach
2	chr8:8492800-8500600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr8:8493400-8506000	Weak transcription	HSMMtube	muscle
4	chr8:8494200-8499200	Enhancers	Primary hematopoietic stem cells	blood
5	chr8:8494200-8499600	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr8:8494400-8500000	Weak transcription	Hela-S3	cervix
7	chr8:8494600-8500400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr8:8494600-8504600	Weak transcription	Right Atrium	heart
9	chr8:8495000-8503000	Weak transcription	Spleen	Spleen
10	chr8:8495200-8500400	Weak transcription	Placenta	Placenta
11	chr8:8495200-8503600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr8:8495600-8499400	Enhancers	A549	lung
13	chr8:8495800-8499200	Enhancers	Fetal Lung	lung
14	chr8:8496200-8499200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr8:8496800-8499200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr8:8497200-8499200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr8:8497200-8499200	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr8:8497200-8499200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr8:8497200-8499400	Enhancers	Primary B cells from peripheral blood	blood
20	chr8:8497400-8499200	Enhancers	Brain Germinal Matrix	brain
21	chr8:8497400-8502800	Weak transcription	Fetal Muscle Leg	muscle
22	chr8:8497600-8499200	Flanking Active TSS	GM12878-XiMat	blood
23	chr8:8498000-8499200	Enhancers	Right Ventricle	heart
24	chr8:8498000-8506600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr8:8498200-8500400	Weak transcription	Brain Anterior Caudate	brain
26	chr8:8498200-8503600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr8:8498400-8499200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr8:8498800-8499200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr8:8498800-8499200	Enhancers	Lung	lung
30	chr8:8498800-8499200	Enhancers	Pancreas	Pancrea
31	chr8:8498800-8499400	Enhancers	Left Ventricle	heart
32	chr8:8499000-8499200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr8:8499000-8499200	Enhancers	Stomach Mucosa	stomach
34	chr8:8499000-8501400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr8:8499000-8502400	Weak transcription	Fetal Brain Male	brain
36	chr8:8499000-8502600	Weak transcription	Adipose Nuclei	Adipose
37	chr8:8499000-8504400	Weak transcription	Fetal Kidney	kidney

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