Variant report

Variant	rs1130569
Chromosome Location	chr8:100899793-100899794
allele	C/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	chr8:100894717..100896294-chr8:100897963..100900047,2	K562	blood:
3	chr8:100894212..100902877-chr8:100903652..100908826,13	MCF-7	breast:
4	chr8:100897606..100900437-chr8:100902962..100907619,5	K562	blood:
5	chr8:100888112..100894632-chr8:100894660..100899830,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164919	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10955222	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10955223	0.81[ASN][1000 genomes]
rs1130474	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1135382	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12544943	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12545930	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12546882	0.83[EUR][1000 genomes]
rs12547260	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12548344	0.83[EUR][1000 genomes]
rs12548542	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12548840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13252579	0.82[ASN][1000 genomes]
rs13253073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13259051	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13259066	0.82[ASN][1000 genomes]
rs13260744	0.80[EUR][1000 genomes]
rs13265660	0.80[EUR][1000 genomes]
rs13271488	0.80[EUR][1000 genomes]
rs13274441	0.82[EUR][1000 genomes]
rs13277184	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs13280341	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2305290	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs34029308	0.81[ASN][1000 genomes]
rs34513504	0.82[EUR][1000 genomes]
rs34830464	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35031559	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35135010	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35935983	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4409375	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4434590	0.87[EUR][1000 genomes]
rs4480092	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4510829	0.88[CEU][hapmap];0.88[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4626565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62534626	0.83[EUR][1000 genomes]
rs62534633	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6468694	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6468695	0.83[EUR][1000 genomes]
rs6468696	0.83[EUR][1000 genomes]
rs7009713	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7015733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7812991	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7824037	0.80[EUR][1000 genomes]
rs7828241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7831963	0.81[EUR][1000 genomes]
rs7832488	0.83[EUR][1000 genomes]
rs7840626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7844439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[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
rs1130569	VPS13B	cis	Thyroid	GTEx
rs1130569	CDKL2	cis	Liver	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	chr8:100880400-100900000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr8:100883200-100901800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr8:100883600-100903200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr8:100883800-100901600	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr8:100883800-100903200	Strong transcription	Duodenum Mucosa	Duodenum
8	chr8:100884400-100904800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:100885200-100903800	Weak transcription	Esophagus	oesophagus
10	chr8:100885600-100904800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr8:100886000-100899800	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr8:100886800-100904000	Weak transcription	Right Ventricle	heart
13	chr8:100886800-100904800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr8:100888200-100900800	Weak transcription	Pancreas	Pancrea
15	chr8:100889400-100901000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr8:100889400-100904800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr8:100890800-100904000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr8:100891400-100904200	Weak transcription	Colonic Mucosa	Colon
19	chr8:100892400-100903400	Weak transcription	Gastric	stomach
20	chr8:100893600-100901400	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr8:100893800-100899800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr8:100893800-100903200	Strong transcription	Liver	Liver
23	chr8:100894000-100903600	Strong transcription	Placenta	Placenta
24	chr8:100894000-100903800	Strong transcription	K562	blood
25	chr8:100894400-100900000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
26	chr8:100894400-100900000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
27	chr8:100894400-100902600	Strong transcription	Primary B cells from peripheral blood	blood
28	chr8:100894600-100901400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr8:100894600-100903800	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr8:100894600-100904000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr8:100895000-100901400	Strong transcription	Adipose Nuclei	Adipose
32	chr8:100895000-100901800	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr8:100895000-100903600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr8:100895200-100899800	Strong transcription	HSMM	muscle
35	chr8:100895200-100900000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr8:100895200-100901600	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr8:100895200-100903600	Strong transcription	Fetal Intestine Large	intestine
38	chr8:100895400-100901400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr8:100895400-100901800	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr8:100895400-100903200	Strong transcription	Fetal Thymus	thymus
41	chr8:100895600-100900600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr8:100895600-100901400	Strong transcription	Primary B cells from cord blood	blood
43	chr8:100895600-100901800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr8:100896000-100900400	Weak transcription	Fetal Intestine Small	intestine
45	chr8:100896000-100903600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr8:100896000-100903800	Weak transcription	Aorta	Aorta
47	chr8:100896400-100902400	Strong transcription	Dnd41	blood
48	chr8:100896400-100903800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr8:100896400-100904000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr8:100896400-100904200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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