Variant report

Variant	rs7828241
Chromosome Location	chr8:100892645-100892646
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:100889851..100891596-chr8:100892250..100894535,2	K562	blood:
2	chr8:100884579..100893900-chr8:100903048..100907419,14	MCF-7	breast:
3	chr8:100891707..100894119-chr8:100903975..100907084,4	MCF-7	breast:
4	chr8:100892119..100896561-chr8:100901220..100906045,8	K562	blood:
5	chr8:100892119..100894804-chr8:100904181..100906017,2	K562	blood:

Variant related genes	Relation type
ENSG00000164919	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10955222	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[ASN][1000 genomes]
rs1130474	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1130569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1135382	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11987173	0.86[EUR][1000 genomes]
rs12541837	0.81[ASN][1000 genomes]
rs12544943	0.82[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs12545930	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12546882	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12548344	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12548542	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12548840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13253073	1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs13259051	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13260744	0.88[EUR][1000 genomes]
rs13265660	0.88[EUR][1000 genomes]
rs13271488	0.88[EUR][1000 genomes]
rs13274441	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13277184	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs13280341	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2305290	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs34513504	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34830464	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35031559	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35135010	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35769167	0.94[ASN][1000 genomes]
rs4409375	1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4434590	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4480092	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4510829	0.83[ASW][hapmap];0.88[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.91[LWK][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4626565	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62534626	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62534633	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6468694	1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6468695	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6468696	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6468697	0.86[ASN][1000 genomes]
rs6984511	0.81[ASN][1000 genomes]
rs7009713	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7015733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7157	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7812991	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7824037	0.88[EUR][1000 genomes]
rs7831963	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7832488	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7840626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7844439	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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
rs7828241	VPS13B	cis	Thyroid	GTEx
rs7828241	VPS13B	Cis_1M	lymphoblastoid	RTeQTL

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	chr8:100858600-100894000	Weak transcription	Fetal Brain Male	brain
3	chr8:100860200-100893000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr8:100868600-100898400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr8:100872000-100898200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr8:100872800-100903800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr8:100877800-100893400	Strong transcription	Primary T cells from cord blood	blood
8	chr8:100880200-100893000	Strong transcription	Primary B cells from cord blood	blood
9	chr8:100880200-100895000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr8:100880400-100900000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr8:100880800-100893000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr8:100881600-100893800	Strong transcription	Primary B cells from peripheral blood	blood
13	chr8:100882000-100895000	Strong transcription	Fetal Thymus	thymus
14	chr8:100882600-100893800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr8:100882800-100892800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr8:100882800-100893000	Strong transcription	Thymus	Thymus
17	chr8:100883000-100896000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr8:100883200-100895000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr8:100883200-100901800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr8:100883600-100895800	Weak transcription	Fetal Heart	heart
21	chr8:100883600-100903200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr8:100883800-100892800	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr8:100883800-100901600	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr8:100883800-100903200	Strong transcription	Duodenum Mucosa	Duodenum
25	chr8:100884400-100895000	Weak transcription	Aorta	Aorta
26	chr8:100884400-100898400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr8:100884400-100904800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr8:100885000-100892800	Strong transcription	Liver	Liver
29	chr8:100885200-100903800	Weak transcription	Esophagus	oesophagus
30	chr8:100885600-100904800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr8:100885800-100895800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr8:100886000-100899800	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr8:100886800-100898200	Weak transcription	Small Intestine	intestine
34	chr8:100886800-100904000	Weak transcription	Right Ventricle	heart
35	chr8:100886800-100904800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr8:100887000-100894200	Weak transcription	Brain Substantia Nigra	brain
37	chr8:100887200-100893000	Strong transcription	HepG2	liver
38	chr8:100888200-100895400	Weak transcription	NHLF	lung
39	chr8:100888200-100898400	Weak transcription	Lung	lung
40	chr8:100888200-100900800	Weak transcription	Pancreas	Pancrea
41	chr8:100888400-100896000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr8:100888600-100893400	Strong transcription	NHDF-Ad	bronchial
43	chr8:100888800-100897400	Weak transcription	HUVEC	blood vessel
44	chr8:100889000-100893600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr8:100889000-100894200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr8:100889000-100897600	Weak transcription	Hela-S3	cervix
47	chr8:100889200-100892800	Strong transcription	HSMM	muscle
48	chr8:100889200-100893200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr8:100889200-100898200	Weak transcription	Brain Angular Gyrus	brain
50	chr8:100889200-100898600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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