Variant report

Variant	rs9834535
Chromosome Location	chr3:49378797-49378798
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49377018-49378824	GM12892	blood:	n/a	n/a
2	POLR2A	chr3:49376950-49378902	HL-60	blood:	n/a	n/a
3	POLR2A	chr3:49377111-49378870	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:49377182-49378825	HL-60	blood:	n/a	n/a
5	POLR2A	chr3:49376948-49378881	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49207496..49209154-chr3:49376769..49379124,2	MCF-7	breast:
2	chr3:49375789..49379333-chr3:49446166..49450939,13	K562	blood:
3	chr3:49376524..49378988-chr3:49507303..49509521,2	MCF-7	breast:
4	chr3:49376764..49379634-chr3:49465144..49467494,3	MCF-7	breast:
5	chr3:49375112..49379681-chr3:49446166..49452291,17	K562	blood:
6	chr3:49377853..49379731-chr3:49460064..49462187,2	K562	blood:
7	chr3:49376293..49379620-chr3:49448851..49451356,3	MCF-7	breast:
8	chr3:49064325..49066470-chr3:49377582..49379875,2	K562	blood:
9	chr3:49377084..49379212-chr3:49447955..49450362,2	MCF-7	breast:

No data

Variant related genes	Relation type
USP4	TF binding region
ENSG00000235261	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000173402	Chromatin interaction
ENSG00000185909	Chromatin interaction
ENSG00000145029	Chromatin interaction
ENSG00000145020	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11130190	0.83[EUR][1000 genomes]
rs11710434	0.84[AMR][1000 genomes]
rs11719762	0.82[EUR][1000 genomes]
rs11720542	0.84[AMR][1000 genomes]
rs11720657	0.83[EUR][1000 genomes]
rs3448	0.83[EUR][1000 genomes]
rs4955424	0.81[EUR][1000 genomes]
rs4955425	0.81[EUR][1000 genomes]
rs4955430	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6446262	0.81[EUR][1000 genomes]
rs6769744	0.82[EUR][1000 genomes]
rs6775069	0.80[EUR][1000 genomes]
rs6784203	0.81[EUR][1000 genomes]
rs6796147	0.83[EUR][1000 genomes]
rs974495	0.82[EUR][1000 genomes]

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs9834535	AMT	cis	Artery Aorta	GTEx
rs9834535	PFKFB4	cis	Nerve Tibial	GTEx
rs9834535	AMT	cis	Esophagus Mucosa	GTEx
rs9834535	AMT	cis	lung	GTEx
rs9834535	AMT	cis	Artery Tibial	GTEx
rs9834535	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs9834535	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs9834535	AMT	cis	Esophagus Muscularis	GTEx
rs9834535	AMT	cis	Muscle Skeletal	GTEx
rs9834535	NICN1-AS1	cis	Thyroid	GTEx
rs9834535	WDR6	cis	Nerve Tibial	GTEx
rs9834535	WDR6	cis	Muscle Skeletal	GTEx
rs9834535	WDR6	cis	Esophagus Muscularis	GTEx
rs9834535	AMT	cis	Adipose Subcutaneous	GTEx
rs9834535	AMT	cis	Whole Blood	GTEx
rs9834535	AMT	cis	Nerve Tibial	GTEx
rs9834535	NICN1	cis	Thyroid	GTEx
rs9834535	AMT	cis	Thyroid	GTEx
rs9834535	NCKIPSD	cis	Esophagus Muscularis	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49376400-49378800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49377600-49378800	Flanking Active TSS	Primary T cells from cord blood	blood
3	chr3:49377600-49378800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr3:49377600-49378800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:49377600-49378800	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr3:49377600-49378800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr3:49377600-49378800	Flanking Active TSS	Dnd41	blood
8	chr3:49377600-49378800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr3:49377600-49379000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr3:49377800-49378800	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr3:49378200-49378800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:49378200-49378800	Enhancers	Esophagus	oesophagus
13	chr3:49378200-49378800	Enhancers	Pancreas	Pancrea
14	chr3:49378200-49378800	Enhancers	HMEC	breast
15	chr3:49378200-49379000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:49378200-49379000	Enhancers	Right Ventricle	heart
17	chr3:49378400-49378800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:49378400-49378800	Enhancers	Brain Angular Gyrus	brain
19	chr3:49378400-49379000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:49378400-49379000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:49378400-49379000	Enhancers	Fetal Heart	heart
22	chr3:49378400-49379000	Enhancers	Spleen	Spleen
23	chr3:49378400-49379600	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr3:49378400-49382400	Enhancers	Primary B cells from peripheral blood	blood
25	chr3:49378600-49378800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:49378600-49378800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr3:49378600-49378800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:49378600-49378800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:49378600-49378800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr3:49378600-49378800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:49378600-49378800	Enhancers	Brain Anterior Caudate	brain
32	chr3:49378600-49378800	Enhancers	Colonic Mucosa	Colon
33	chr3:49378600-49378800	Enhancers	Colon Smooth Muscle	Colon
34	chr3:49378600-49378800	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr3:49378600-49378800	Enhancers	Fetal Lung	lung
36	chr3:49378600-49378800	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr3:49378600-49378800	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr3:49378600-49378800	Enhancers	Small Intestine	intestine
39	chr3:49378600-49378800	Enhancers	Stomach Smooth Muscle	stomach
40	chr3:49378600-49378800	Active TSS	Hela-S3	cervix
41	chr3:49378600-49378800	Active TSS	HepG2	liver
42	chr3:49378600-49378800	Enhancers	HUVEC	blood vessel
43	chr3:49378600-49379000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:49378600-49379000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:49378600-49379000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:49378600-49379000	Enhancers	Fetal Intestine Large	intestine
47	chr3:49378600-49379000	Enhancers	Fetal Intestine Small	intestine
48	chr3:49378600-49379000	Enhancers	Fetal Stomach	stomach
49	chr3:49378600-49379000	Enhancers	Left Ventricle	heart
50	chr3:49378600-49379000	Enhancers	Lung	lung

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