Variant report

Variant	rs1130474
Chromosome Location	chr8:100904277-100904278
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	chr8:100904036..100906374-chr8:101015983..101018100,2	MCF-7	breast:
2	chr8:100884579..100893900-chr8:100903048..100907419,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212414	Chromatin interaction
ENSG00000164919	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10955223	0.85[ASN][1000 genomes]
rs1130569	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1135382	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12544943	0.84[ASN][1000 genomes]
rs12545930	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12546882	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12547260	0.99[ASN][1000 genomes]
rs12548344	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12548542	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12548840	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13252579	0.84[ASN][1000 genomes]
rs13253073	0.84[ASN][1000 genomes]
rs13259051	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13259066	0.81[ASN][1000 genomes]
rs13274441	0.81[EUR][1000 genomes]
rs13277184	0.99[ASN][1000 genomes]
rs13280341	0.84[ASN][1000 genomes]
rs34029308	0.85[ASN][1000 genomes]
rs34513504	0.81[EUR][1000 genomes]
rs34771613	0.81[AFR][1000 genomes]
rs34830464	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35031559	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35135010	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35935983	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4434590	0.86[EUR][1000 genomes]
rs4510829	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4626565	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62534626	0.82[EUR][1000 genomes]
rs62534633	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6468695	0.82[EUR][1000 genomes]
rs6468696	0.82[EUR][1000 genomes]
rs7009713	0.82[EUR][1000 genomes]
rs7015733	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7157	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7812991	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7828241	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7831963	0.80[EUR][1000 genomes]
rs7832488	0.82[EUR][1000 genomes]
rs7840626	0.81[EUR][1000 genomes]
rs7844439	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[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
rs1130474	VPS13B	Cis_1M	lymphoblastoid	RTeQTL
rs1130474	VPS13B	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:100884400-100904800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:100885600-100904800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr8:100886800-100904800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr8:100889400-100904800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr8:100899800-100904600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr8:100901200-100904400	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr8:100902000-100904800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr8:100902400-100904400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr8:100902600-100904400	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr8:100902600-100904400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr8:100902600-100904600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr8:100902600-100904600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr8:100902600-100904800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr8:100902800-100904400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr8:100903200-100904400	Enhancers	Fetal Heart	heart
16	chr8:100903400-100904400	Enhancers	Primary T cells fromperipheralblood	blood
17	chr8:100903400-100904400	Enhancers	Brain Substantia Nigra	brain
18	chr8:100903400-100904400	Enhancers	Fetal Brain Male	brain
19	chr8:100903400-100904600	Enhancers	Gastric	stomach
20	chr8:100903400-100906200	Active TSS	GM12878-XiMat	blood
21	chr8:100903600-100904400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr8:100903600-100904400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr8:100903600-100904400	Enhancers	Fetal Brain Female	brain
24	chr8:100903800-100904400	Enhancers	Aorta	Aorta
25	chr8:100903800-100904400	Enhancers	Fetal Intestine Large	intestine
26	chr8:100903800-100904400	Enhancers	HSMMtube	muscle
27	chr8:100903800-100904600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr8:100903800-100904600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr8:100903800-100904600	Enhancers	Esophagus	oesophagus
30	chr8:100903800-100904600	Genic enhancers	Fetal Muscle Leg	muscle
31	chr8:100903800-100904600	Enhancers	Lung	lung
32	chr8:100903800-100904600	Flanking Active TSS	Rectal Smooth Muscle	rectum
33	chr8:100903800-100904800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr8:100903800-100904800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr8:100903800-100904800	Enhancers	Small Intestine	intestine
36	chr8:100903800-100904800	Enhancers	Stomach Mucosa	stomach
37	chr8:100903800-100905000	Enhancers	Spleen	Spleen
38	chr8:100903800-100905200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr8:100903800-100905200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr8:100903800-100905200	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr8:100903800-100905400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr8:100903800-100906200	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr8:100904000-100904400	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr8:100904000-100904400	Enhancers	Muscle Satellite Cultured Cells	--
45	chr8:100904000-100904400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr8:100904000-100904400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr8:100904000-100904400	Enhancers	HSMM	muscle
48	chr8:100904000-100904400	Enhancers	HUVEC	blood vessel
49	chr8:100904000-100904600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr8:100904000-100904600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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