Variant report

Variant	rs12545930
Chromosome Location	chr8:100900356-100900357
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:100894717..100897458-chr8:100897759..100900943,4	K562	blood:
2	chr8:100894212..100902877-chr8:100903652..100908826,13	MCF-7	breast:
3	chr8:100897606..100900437-chr8:100902962..100907619,5	K562	blood:

Variant related genes	Relation type
ENSG00000164919	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1130474	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1130569	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1135382	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12547260	0.90[ASN][1000 genomes]
rs12548542	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12548840	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13259051	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13277184	0.90[ASN][1000 genomes]
rs35031559	0.81[EUR][1000 genomes]
rs35135010	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4510829	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4626565	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62534633	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7015733	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7157	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7812991	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7828241	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7844439	0.83[AMR][1000 genomes];0.82[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
rs12545930	VPS13B	Cis_1M	lymphoblastoid	RTeQTL
rs12545930	VPS13B	cis	Thyroid	GTEx

Chromatin state (count:126 , 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	chr8:100883800-100901600	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr8:100883800-100903200	Strong transcription	Duodenum Mucosa	Duodenum
7	chr8:100884400-100904800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr8:100885200-100903800	Weak transcription	Esophagus	oesophagus
9	chr8:100885600-100904800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr8:100886800-100904000	Weak transcription	Right Ventricle	heart
11	chr8:100886800-100904800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr8:100888200-100900800	Weak transcription	Pancreas	Pancrea
13	chr8:100889400-100901000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr8:100889400-100904800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr8:100890800-100904000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr8:100891400-100904200	Weak transcription	Colonic Mucosa	Colon
17	chr8:100892400-100903400	Weak transcription	Gastric	stomach
18	chr8:100893600-100901400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr8:100893800-100903200	Strong transcription	Liver	Liver
20	chr8:100894000-100903600	Strong transcription	Placenta	Placenta
21	chr8:100894000-100903800	Strong transcription	K562	blood
22	chr8:100894400-100902600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr8:100894600-100901400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr8:100894600-100903800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr8:100894600-100904000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr8:100895000-100901400	Strong transcription	Adipose Nuclei	Adipose
27	chr8:100895000-100901800	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr8:100895000-100903600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr8:100895200-100901600	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr8:100895200-100903600	Strong transcription	Fetal Intestine Large	intestine
31	chr8:100895400-100901400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr8:100895400-100901800	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr8:100895400-100903200	Strong transcription	Fetal Thymus	thymus
34	chr8:100895600-100900600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr8:100895600-100901400	Strong transcription	Primary B cells from cord blood	blood
36	chr8:100895600-100901800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr8:100896000-100900400	Weak transcription	Fetal Intestine Small	intestine
38	chr8:100896000-100903600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr8:100896000-100903800	Weak transcription	Aorta	Aorta
40	chr8:100896400-100902400	Strong transcription	Dnd41	blood
41	chr8:100896400-100903800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr8:100896400-100904000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr8:100896400-100904200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr8:100896600-100902600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr8:100896600-100902600	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr8:100896600-100903800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr8:100897000-100904000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr8:100897200-100902800	Strong transcription	NHEK	skin
49	chr8:100897200-100903800	Strong transcription	Fetal Muscle Leg	muscle
50	chr8:100897400-100901000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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