Variant report

Variant	rs1563564
Chromosome Location	chr8:119128860-119128861
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr8:119128388-119128877	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:119123665..119126996-chr8:119127201..119129943,4	MCF-7	breast:

Variant related genes	Relation type
EXT1	TF binding region
ENSG00000182197	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10102634	1.00[CEU][hapmap];0.80[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs10106398	0.90[EUR][1000 genomes]
rs1457201	0.93[ASN][1000 genomes]
rs17454315	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17477441	0.84[CHB][hapmap]
rs2445912	0.94[ASN][1000 genomes]
rs2445923	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2451140	0.83[CEU][hapmap]
rs2451141	0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2451143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451167	0.88[ASN][1000 genomes]
rs2468139	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2468140	0.92[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs2468153	0.98[ASN][1000 genomes]
rs2468154	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2468155	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2514760	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2514761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2514762	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs28421966	0.92[EUR][1000 genomes]
rs726960	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030459	chr8:118840179-119155835	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv612047	chr8:118939094-119468609	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1015380	chr8:118948652-119418389	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv539736	chr8:118948652-119418389	Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv831441	chr8:119055370-119262970	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	esv2752195	chr8:119058819-119139819	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv821660	chr8:119082062-119312183	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv891412	chr8:119107051-119139385	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1563564	SNTB1	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:119124800-119136200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:119125000-119134200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr8:119125400-119129000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr8:119125400-119129400	Enhancers	HMEC	breast
5	chr8:119125400-119138200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr8:119125800-119132000	Weak transcription	NH-A	brain
7	chr8:119125800-119132200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr8:119125800-119132600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr8:119125800-119134800	Weak transcription	Esophagus	oesophagus
10	chr8:119125800-119149600	Weak transcription	Aorta	Aorta
11	chr8:119126000-119130200	Weak transcription	Fetal Intestine Small	intestine
12	chr8:119126200-119129000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr8:119126200-119131800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr8:119126200-119137400	Weak transcription	Lung	lung
15	chr8:119126400-119130000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr8:119126400-119131200	Weak transcription	NHLF	lung
17	chr8:119126400-119131400	Weak transcription	NHDF-Ad	bronchial
18	chr8:119126400-119132000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr8:119126400-119132000	Weak transcription	Fetal Muscle Leg	muscle
20	chr8:119127800-119129200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr8:119128000-119129000	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr8:119128000-119129200	Enhancers	NHEK	skin
23	chr8:119128200-119129000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr8:119128200-119129000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr8:119128200-119130600	Enhancers	Primary T cells from cord blood	blood
26	chr8:119128400-119129200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr8:119128400-119129200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr8:119128400-119129200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr8:119128400-119129800	Enhancers	GM12878-XiMat	blood
30	chr8:119128600-119129000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr8:119128600-119129000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr8:119128600-119129000	Enhancers	Primary T cells fromperipheralblood	blood
33	chr8:119128600-119129000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr8:119128600-119129000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr8:119128600-119129000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr8:119128600-119129000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr8:119128600-119129000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr8:119128600-119129000	Flanking Active TSS	Dnd41	blood
39	chr8:119128600-119129000	Enhancers	HepG2	liver
40	chr8:119128600-119129200	Enhancers	Thymus	Thymus
41	chr8:119128600-119129400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr8:119128600-119129600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr8:119128600-119132200	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr8:119128600-119134000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr8:119128800-119129000	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr8:119128800-119129000	Enhancers	Fetal Thymus	thymus
47	chr8:119128800-119132200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr8:119128800-119134200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr8:119128800-119134600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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