Variant report

Variant	rs4718480
Chromosome Location	chr7:66671807-66671808
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11971398	0.83[AMR][1000 genomes]
rs12530524	0.88[AMR][1000 genomes]
rs12530782	0.88[AMR][1000 genomes]
rs12532995	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12537561	0.90[ASN][1000 genomes]
rs12537954	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12540794	0.88[AMR][1000 genomes]
rs62464964	0.88[AMR][1000 genomes]
rs62464966	0.88[AMR][1000 genomes]
rs62464972	0.88[AMR][1000 genomes]
rs62464974	0.88[AMR][1000 genomes]
rs62464975	0.88[AMR][1000 genomes]
rs62464976	1.00[AMR][1000 genomes]
rs62465000	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62465002	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465005	0.90[ASN][1000 genomes]
rs62465013	0.88[AMR][1000 genomes]
rs62465014	0.88[AMR][1000 genomes]
rs62465017	0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv888330	chr7:66502171-66877880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
4	nsv831019	chr7:66516808-66720485	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	9 gene(s)	inside rSNPs	diseases
5	esv2422035	chr7:66621964-66676630	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1032237	chr7:66644492-66785029	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv970518	chr7:66647675-66742783	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4718480	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL
rs4718480	RABGEF1	cis	multi-tissue	Pritchard
rs4718480	hmm32897	cis	multi-tissue	Pritchard

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66621600-66672000	Weak transcription	Fetal Intestine Large	intestine
2	chr7:66628600-66684600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr7:66640600-66677200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr7:66644400-66683000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr7:66647000-66677400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr7:66648200-66679800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr7:66649200-66677200	Weak transcription	Right Ventricle	heart
8	chr7:66649200-66679200	Weak transcription	NHEK	skin
9	chr7:66651200-66675400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr7:66652800-66675600	Weak transcription	Aorta	Aorta
11	chr7:66654400-66677400	Weak transcription	Esophagus	oesophagus
12	chr7:66654400-66681600	Weak transcription	Spleen	Spleen
13	chr7:66654600-66678200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:66654600-66683400	Weak transcription	Pancreas	Pancrea
15	chr7:66654600-66684600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr7:66654600-66704600	Weak transcription	Gastric	stomach
17	chr7:66654600-66709600	Weak transcription	Lung	lung
18	chr7:66655000-66675400	Weak transcription	Thymus	Thymus
19	chr7:66656000-66677000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr7:66656400-66672400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr7:66656400-66676000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr7:66656600-66675400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr7:66658000-66673600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr7:66658000-66703200	Weak transcription	Ovary	ovary
25	chr7:66658200-66672200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr7:66658200-66672800	Weak transcription	Psoas Muscle	Psoas
27	chr7:66658200-66678600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr7:66658400-66677400	Weak transcription	Liver	Liver
29	chr7:66658400-66678200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr7:66658600-66674000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr7:66658600-66675400	Weak transcription	Brain Hippocampus Middle	brain
32	chr7:66658600-66677400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr7:66658600-66677400	Weak transcription	Brain Substantia Nigra	brain
34	chr7:66658600-66678600	Weak transcription	A549	lung
35	chr7:66658600-66679600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr7:66658600-66691000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr7:66658800-66677400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr7:66659000-66675400	Weak transcription	HSMMtube	muscle
39	chr7:66659000-66678200	Weak transcription	Left Ventricle	heart
40	chr7:66660000-66675400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr7:66660400-66674000	Weak transcription	Fetal Lung	lung
42	chr7:66660400-66675400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr7:66660400-66675400	Weak transcription	Adipose Nuclei	Adipose
44	chr7:66660400-66675600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr7:66660400-66677000	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr7:66660600-66676400	Weak transcription	Fetal Brain Female	brain
47	chr7:66660600-66677400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr7:66660600-66701600	Weak transcription	Fetal Kidney	kidney
49	chr7:66660600-66703000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr7:66660800-66674600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links