Variant report

Variant	rs552472
Chromosome Location	chr3:43135058-43135059
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	chr3:43134780..43136481-chr3:43146074..43148519,2	MCF-7	breast:
2	chr3:43134162..43136629-chr3:43143357..43147810,4	K562	blood:

Variant related genes	Relation type
ENSG00000144647	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10865926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11129985	1.00[ASW][hapmap]
rs4683359	0.92[AFR][1000 genomes]
rs483765	1.00[ASW][hapmap]
rs491970	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs503100	0.89[MKK][hapmap]
rs513065	1.00[ASW][hapmap]
rs535994	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs614993	1.00[YRI][hapmap]
rs632013	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs664197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs674118	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs939436	0.95[AFR][1000 genomes]
rs9828191	0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv834672	chr3:43132722-43306272	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs552472	ARHGAP25	trans	lymphoblastoid	seeQTL
rs552472	HHEX	trans	lymphoblastoid	seeQTL
rs552472	CD4	trans	lymphoblastoid	seeQTL
rs552472	PLEKHF2	trans	lymphoblastoid	seeQTL
rs552472	UBASH3B	trans	lymphoblastoid	seeQTL
rs552472	OSBPL10	trans	lymphoblastoid	seeQTL
rs552472	PTK2	trans	lymphoblastoid	seeQTL
rs552472	ITGAX	trans	lymphoblastoid	seeQTL
rs552472	CA8	trans	lymphoblastoid	seeQTL
rs552472	BANK1	trans	lymphoblastoid	seeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43119800-43143800	Weak transcription	Fetal Heart	heart
2	chr3:43122400-43145800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr3:43122600-43145200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr3:43122800-43136000	Weak transcription	Pancreas	Pancrea
5	chr3:43122800-43136400	Weak transcription	HSMMtube	muscle
6	chr3:43122800-43145600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:43123000-43135200	Weak transcription	Brain Angular Gyrus	brain
8	chr3:43123000-43136000	Weak transcription	Right Ventricle	heart
9	chr3:43123000-43144400	Weak transcription	Fetal Intestine Large	intestine
10	chr3:43123000-43146400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr3:43123000-43146600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:43123200-43140400	Weak transcription	Gastric	stomach
13	chr3:43123200-43144400	Weak transcription	Spleen	Spleen
14	chr3:43123200-43145000	Weak transcription	Adipose Nuclei	Adipose
15	chr3:43123400-43146400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:43123600-43135400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:43123600-43143600	Weak transcription	Lung	lung
18	chr3:43123600-43146600	Weak transcription	Fetal Intestine Small	intestine
19	chr3:43123800-43136400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:43124200-43135600	Weak transcription	Fetal Brain Female	brain
21	chr3:43124200-43145000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:43124400-43135600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:43124400-43136200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:43124400-43136200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:43124400-43144200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr3:43124400-43146000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:43124400-43146600	Weak transcription	Aorta	Aorta
28	chr3:43124600-43138600	Weak transcription	Thymus	Thymus
29	chr3:43124600-43144800	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr3:43124600-43146800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr3:43127000-43144400	Weak transcription	Dnd41	blood
32	chr3:43129000-43139600	Weak transcription	Liver	Liver
33	chr3:43129200-43136000	Weak transcription	Esophagus	oesophagus
34	chr3:43129200-43144000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr3:43131600-43136600	Weak transcription	Fetal Stomach	stomach
36	chr3:43131600-43145600	Weak transcription	Primary T cells from cord blood	blood
37	chr3:43132600-43135200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:43132600-43146000	Weak transcription	Fetal Lung	lung
39	chr3:43132800-43144000	Weak transcription	Stomach Mucosa	stomach
40	chr3:43133800-43135200	Enhancers	Ovary	ovary
41	chr3:43134400-43135400	Enhancers	Left Ventricle	heart
42	chr3:43134400-43137000	Enhancers	Brain Hippocampus Middle	brain
43	chr3:43134600-43135200	Enhancers	Fetal Muscle Trunk	muscle
44	chr3:43134600-43136800	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr3:43134600-43137000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:43134600-43137000	Enhancers	Brain Cingulate Gyrus	brain
47	chr3:43134600-43137000	Enhancers	Right Atrium	heart
48	chr3:43134600-43137400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:43134600-43137800	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr3:43134600-43139600	Enhancers	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links