Variant report

Variant	rs13259051
Chromosome Location	chr8:100901663-100901664
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	chr8:100894212..100902877-chr8:100903652..100908826,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164919	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10955223	0.82[ASN][1000 genomes]
rs1130474	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1130569	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1135382	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12544943	0.84[ASN][1000 genomes]
rs12545930	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12546882	0.81[EUR][1000 genomes]
rs12547260	0.99[ASN][1000 genomes]
rs12548344	0.81[EUR][1000 genomes]
rs12548542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12548840	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13252579	0.84[ASN][1000 genomes]
rs13253073	0.84[ASN][1000 genomes]
rs13259066	0.84[ASN][1000 genomes]
rs13274441	0.80[EUR][1000 genomes]
rs13277184	0.99[ASN][1000 genomes]
rs13280341	0.84[ASN][1000 genomes]
rs34029308	0.82[ASN][1000 genomes]
rs34513504	0.80[EUR][1000 genomes]
rs34830464	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35031559	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35135010	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35935983	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4434590	0.85[EUR][1000 genomes]
rs4510829	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4626565	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62534626	0.81[EUR][1000 genomes]
rs62534633	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6468695	0.81[EUR][1000 genomes]
rs6468696	0.81[EUR][1000 genomes]
rs7009713	0.81[EUR][1000 genomes]
rs7015733	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7157	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7812991	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7828241	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7832488	0.81[EUR][1000 genomes]
rs7840626	0.91[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7844439	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033944	chr8:100737321-100916345	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv1830910	chr8:100791156-101114794	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13259051	VPS13B	Cis_1M	lymphoblastoid	RTeQTL
rs13259051	VPS13B	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:100846400-100903800	Weak transcription	Stomach Mucosa	stomach
2	chr8:100872800-100903800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr8:100883200-100901800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr8:100883600-100903200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr8:100883800-100903200	Strong transcription	Duodenum Mucosa	Duodenum
6	chr8:100884400-100904800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr8:100885200-100903800	Weak transcription	Esophagus	oesophagus
8	chr8:100885600-100904800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr8:100886800-100904000	Weak transcription	Right Ventricle	heart
10	chr8:100886800-100904800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr8:100889400-100904800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr8:100890800-100904000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr8:100891400-100904200	Weak transcription	Colonic Mucosa	Colon
14	chr8:100892400-100903400	Weak transcription	Gastric	stomach
15	chr8:100893800-100903200	Strong transcription	Liver	Liver
16	chr8:100894000-100903600	Strong transcription	Placenta	Placenta
17	chr8:100894000-100903800	Strong transcription	K562	blood
18	chr8:100894400-100902600	Strong transcription	Primary B cells from peripheral blood	blood
19	chr8:100894600-100903800	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr8:100894600-100904000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr8:100895000-100901800	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr8:100895000-100903600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr8:100895200-100903600	Strong transcription	Fetal Intestine Large	intestine
24	chr8:100895400-100901800	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr8:100895400-100903200	Strong transcription	Fetal Thymus	thymus
26	chr8:100895600-100901800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr8:100896000-100903600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr8:100896000-100903800	Weak transcription	Aorta	Aorta
29	chr8:100896400-100902400	Strong transcription	Dnd41	blood
30	chr8:100896400-100903800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr8:100896400-100904000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr8:100896400-100904200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr8:100896600-100902600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr8:100896600-100902600	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr8:100896600-100903800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr8:100897000-100904000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr8:100897200-100902800	Strong transcription	NHEK	skin
38	chr8:100897200-100903800	Strong transcription	Fetal Muscle Leg	muscle
39	chr8:100897400-100902600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr8:100897400-100903400	Weak transcription	Colon Smooth Muscle	Colon
41	chr8:100897800-100903200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr8:100897800-100903400	Strong transcription	Fetal Lung	lung
43	chr8:100898200-100903200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr8:100898200-100903600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr8:100898400-100902600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr8:100898400-100902600	Weak transcription	Brain Angular Gyrus	brain
47	chr8:100898400-100902800	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr8:100898400-100904000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr8:100898600-100903200	Strong transcription	GM12878-XiMat	blood
50	chr8:100898600-100904200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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