Variant report

Variant	rs12548840
Chromosome Location	chr8:100897808-100897809
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	chr8:100880536..100883479-chr8:100897737..100899269,2	MCF-7	breast:
3	chr8:100884824..100892644-chr8:100893035..100898691,10	K562	blood:
4	chr8:100894212..100902877-chr8:100903652..100908826,13	MCF-7	breast:
5	chr8:100897606..100900437-chr8:100902962..100907619,5	K562	blood:
6	chr8:100888112..100894632-chr8:100894660..100899830,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164919	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10955222	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10955223	0.82[ASN][1000 genomes]
rs1130474	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1130569	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]
rs1135382	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12544943	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs12545930	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12546882	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12547260	0.99[ASN][1000 genomes]
rs12548344	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12548542	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13252579	0.84[ASN][1000 genomes]
rs13253073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13259051	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13259066	0.84[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];0.99[ASN][1000 genomes]
rs13280341	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2305290	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs34029308	0.82[ASN][1000 genomes]
rs34513504	0.82[EUR][1000 genomes]
rs34771613	0.82[AFR][1000 genomes]
rs34830464	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35031559	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35135010	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35935983	0.82[AMR][1000 genomes];0.85[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];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4626565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];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];0.99[ASN][1000 genomes]
rs6468694	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6468695	0.83[EUR][1000 genomes]
rs6468696	0.83[EUR][1000 genomes]
rs6468697	0.81[AFR][1000 genomes]
rs7009713	0.83[EUR][1000 genomes]
rs7015733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7812991	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7824037	0.80[EUR][1000 genomes]
rs7828241	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]
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];1.00[YRI][hapmap];0.92[AFR][1000 genomes];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
rs12548840	VPS13B	Cis_1M	lymphoblastoid	RTeQTL
rs12548840	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	chr8:100868600-100898400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr8:100872000-100898200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr8:100872800-100903800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr8:100880400-100900000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr8:100883200-100901800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr8:100883600-100903200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr8:100883800-100901600	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr8:100883800-100903200	Strong transcription	Duodenum Mucosa	Duodenum
10	chr8:100884400-100898400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr8:100884400-100904800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr8:100885200-100903800	Weak transcription	Esophagus	oesophagus
13	chr8:100885600-100904800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr8:100886000-100899800	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr8:100886800-100898200	Weak transcription	Small Intestine	intestine
16	chr8:100886800-100904000	Weak transcription	Right Ventricle	heart
17	chr8:100886800-100904800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr8:100888200-100898400	Weak transcription	Lung	lung
19	chr8:100888200-100900800	Weak transcription	Pancreas	Pancrea
20	chr8:100889200-100898200	Weak transcription	Brain Angular Gyrus	brain
21	chr8:100889200-100898600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr8:100889400-100898200	Weak transcription	Spleen	Spleen
23	chr8:100889400-100901000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr8:100889400-100904800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr8:100889600-100898200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr8:100890800-100898400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr8:100890800-100904000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr8:100891400-100904200	Weak transcription	Colonic Mucosa	Colon
29	chr8:100892400-100898200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr8:100892400-100903400	Weak transcription	Gastric	stomach
31	chr8:100892800-100898800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr8:100893000-100899200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr8:100893400-100899200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
34	chr8:100893600-100898400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr8:100893600-100898600	ZNF genes & repeats	GM12878-XiMat	blood
36	chr8:100893600-100901400	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr8:100893800-100899800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr8:100893800-100903200	Strong transcription	Liver	Liver
39	chr8:100894000-100903600	Strong transcription	Placenta	Placenta
40	chr8:100894000-100903800	Strong transcription	K562	blood
41	chr8:100894400-100900000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
42	chr8:100894400-100900000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
43	chr8:100894400-100902600	Strong transcription	Primary B cells from peripheral blood	blood
44	chr8:100894600-100898000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr8:100894600-100898000	Weak transcription	HMEC	breast
46	chr8:100894600-100898200	Weak transcription	Brain Substantia Nigra	brain
47	chr8:100894600-100901400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr8:100894600-100903800	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr8:100894600-100904000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr8:100895000-100899200	Strong transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links