Variant report

Variant	rs11709289
Chromosome Location	chr3:47806649-47806650
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:47806554-47806752	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47803418..47807540-chr3:47810492..47813252,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266457	TF binding region
ENSG00000266457	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11716779	0.86[AMR][1000 genomes]
rs13072132	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17785248	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34448818	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34507589	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35012836	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5016900	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260764	0.82[AFR][1000 genomes]
rs62262084	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003072	chr3:47673628-47869154	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv876758	chr3:47681881-47842234	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
3	nsv876759	chr3:47725315-47830741	Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
4	nsv834679	chr3:47749475-47924006	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
5	nsv590233	chr3:47798700-47829277	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs11709289	ZNF589	cis	Artery Tibial	GTEx
rs11709289	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs11709289	MRPS18AP1	cis	Artery Tibial	GTEx
rs11709289	ZNF589	cis	Esophagus Muscularis	GTEx
rs11709289	CDC25A	cis	Muscle Skeletal	GTEx
rs11709289	MRPS18AP1	cis	Nerve Tibial	GTEx
rs11709289	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs11709289	SMARCC1	Cis_1M	lymphoblastoid	RTeQTL
rs11709289	MRPS18AP1	cis	Thyroid	GTEx
rs11709289	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs11709289	ZNF589	cis	Nerve Tibial	GTEx
rs11709289	NME6	cis	Esophagus Muscularis	GTEx
rs11709289	MAP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47701600-47819800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:47727600-47819400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:47769600-47812400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:47769800-47817800	Weak transcription	Pancreas	Pancrea
5	chr3:47772800-47821000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:47774200-47820600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:47777000-47817600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr3:47777200-47812400	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:47777200-47813600	Weak transcription	A549	lung
10	chr3:47777200-47819000	Weak transcription	Fetal Brain Male	brain
11	chr3:47777200-47819800	Weak transcription	Small Intestine	intestine
12	chr3:47777400-47812600	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:47777400-47819800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:47777400-47821000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:47777400-47821000	Weak transcription	Brain Substantia Nigra	brain
16	chr3:47777400-47821800	Weak transcription	Right Ventricle	heart
17	chr3:47777600-47812800	Weak transcription	NHDF-Ad	bronchial
18	chr3:47777600-47820600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:47777600-47820800	Weak transcription	NHLF	lung
20	chr3:47778800-47814200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:47784000-47816000	Strong transcription	Fetal Stomach	stomach
22	chr3:47784400-47811800	Weak transcription	Left Ventricle	heart
23	chr3:47784800-47820800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:47786600-47814200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:47787200-47808200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:47787200-47811000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:47787400-47808000	Weak transcription	Adipose Nuclei	Adipose
28	chr3:47787400-47811800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:47787400-47812600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:47787400-47820800	Weak transcription	Brain Angular Gyrus	brain
31	chr3:47788000-47813600	Weak transcription	HUVEC	blood vessel
32	chr3:47793000-47818000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:47793800-47814800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr3:47794000-47807600	Weak transcription	Osteobl	bone
35	chr3:47794600-47811800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:47794800-47819400	Weak transcription	Right Atrium	heart
37	chr3:47795800-47814600	Strong transcription	Fetal Thymus	thymus
38	chr3:47796800-47807600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:47797800-47814600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:47798000-47815000	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:47798000-47816600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr3:47798600-47812400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:47798800-47808600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:47798800-47821000	Weak transcription	Brain Anterior Caudate	brain
45	chr3:47799000-47812600	Weak transcription	Hela-S3	cervix
46	chr3:47799600-47808200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:47800000-47820800	Weak transcription	HSMMtube	muscle
48	chr3:47800200-47808400	Strong transcription	Fetal Intestine Large	intestine
49	chr3:47800200-47809800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:47800400-47813000	Weak transcription	Spleen	Spleen

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