Variant report

Variant	rs62467421
Chromosome Location	chr7:65542374-65542375
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	chr7:65540799..65542994-chr7:65578683..65581272,2	MCF-7	breast:
2	chr7:65540457..65542538-chr7:65550059..65552910,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000126522	Chromatin interaction
ENSG00000249319	Chromatin interaction
ENSG00000241258	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs12530898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12531358	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12531900	1.00[AFR][1000 genomes]
rs12532327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12532423	1.00[AFR][1000 genomes]
rs12532675	1.00[AFR][1000 genomes]
rs12534109	1.00[AFR][1000 genomes]
rs12534477	1.00[AFR][1000 genomes]
rs12534881	1.00[AFR][1000 genomes]
rs12535985	1.00[AFR][1000 genomes]
rs12536292	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12537407	1.00[AMR][1000 genomes]
rs12537936	1.00[AFR][1000 genomes]
rs12538025	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12538147	1.00[AFR][1000 genomes]
rs12538379	1.00[AFR][1000 genomes]
rs12538961	1.00[AFR][1000 genomes]
rs12540888	1.00[AFR][1000 genomes]
rs2279904	1.00[AFR][1000 genomes]
rs2292936	1.00[AFR][1000 genomes]
rs2292937	1.00[AFR][1000 genomes]
rs35832738	1.00[AFR][1000 genomes]
rs3735141	1.00[AFR][1000 genomes]
rs62465474	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62465475	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62465476	1.00[AFR][1000 genomes]
rs62465483	1.00[AFR][1000 genomes]
rs62465484	1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs62465512	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62465513	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62465515	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62465519	1.00[AFR][1000 genomes]
rs62465521	1.00[AFR][1000 genomes]
rs62465522	1.00[AFR][1000 genomes]
rs62465525	1.00[AFR][1000 genomes]
rs62465526	1.00[AFR][1000 genomes]
rs62465527	1.00[AFR][1000 genomes]
rs62465542	1.00[AFR][1000 genomes]
rs62465545	1.00[AFR][1000 genomes]
rs62465546	1.00[AFR][1000 genomes]
rs62465547	1.00[AFR][1000 genomes]
rs62465550	1.00[AFR][1000 genomes]
rs62465552	1.00[AFR][1000 genomes]
rs62465554	1.00[AFR][1000 genomes]
rs62467382	1.00[AFR][1000 genomes]
rs62467384	1.00[AFR][1000 genomes]
rs62467385	1.00[AFR][1000 genomes]
rs62467386	1.00[AFR][1000 genomes]
rs62467410	1.00[AFR][1000 genomes]
rs62467411	1.00[AFR][1000 genomes]
rs62467413	1.00[AFR][1000 genomes]
rs62467414	1.00[AFR][1000 genomes]
rs62467436	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62467437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62467441	1.00[AMR][1000 genomes]
rs62467442	1.00[AMR][1000 genomes]
rs62467444	1.00[AMR][1000 genomes]
rs62467450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62468669	1.00[AFR][1000 genomes]
rs62468673	1.00[AFR][1000 genomes]
rs62468674	1.00[AFR][1000 genomes]
rs62468677	1.00[AFR][1000 genomes]
rs62470879	1.00[AFR][1000 genomes]
rs62470880	1.00[AFR][1000 genomes]
rs62470886	1.00[AFR][1000 genomes]
rs62470891	1.00[AFR][1000 genomes]
rs62470894	1.00[AFR][1000 genomes]
rs62470895	1.00[AFR][1000 genomes]
rs62470897	1.00[AFR][1000 genomes]
rs62470899	1.00[AFR][1000 genomes]
rs62470900	1.00[AFR][1000 genomes]
rs62470921	1.00[AFR][1000 genomes]
rs62470922	1.00[AFR][1000 genomes]
rs62470924	1.00[AFR][1000 genomes]
rs62470925	1.00[AFR][1000 genomes]
rs62470926	1.00[AFR][1000 genomes]
rs62470931	1.00[AFR][1000 genomes]
rs62470934	1.00[AFR][1000 genomes]
rs62470940	1.00[AFR][1000 genomes]
rs62470945	1.00[AFR][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	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
3	nsv888325	chr7:65474919-65575893	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1021186	chr7:65492601-65663438	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv984546	chr7:65531382-65556631	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62467421	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65540400-65542800	Active TSS	Fetal Intestine Large	intestine
2	chr7:65540600-65542800	Active TSS	Liver	Liver
3	chr7:65540800-65542400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:65541200-65542400	Flanking Active TSS	Colonic Mucosa	Colon
5	chr7:65541200-65542400	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr7:65541200-65542400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
7	chr7:65541200-65542400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
8	chr7:65541600-65542400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr7:65541600-65542400	Enhancers	Primary B cells from peripheral blood	blood
10	chr7:65541600-65542400	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr7:65541600-65542400	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
12	chr7:65541600-65543000	Enhancers	Fetal Heart	heart
13	chr7:65541600-65543200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:65541600-65543200	Enhancers	Primary T cells fromperipheralblood	blood
15	chr7:65541600-65543400	Enhancers	Spleen	Spleen
16	chr7:65541600-65549600	Weak transcription	Thymus	Thymus
17	chr7:65541600-65565000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr7:65541800-65542400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr7:65541800-65542400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr7:65541800-65542400	Enhancers	Fetal Muscle Trunk	muscle
21	chr7:65541800-65542400	Active TSS	Rectal Smooth Muscle	rectum
22	chr7:65541800-65542400	Flanking Active TSS	HepG2	liver
23	chr7:65541800-65543000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr7:65541800-65543200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr7:65541800-65543200	Weak transcription	Esophagus	oesophagus
26	chr7:65541800-65546600	Weak transcription	Primary T cells from cord blood	blood
27	chr7:65541800-65551000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr7:65541800-65554200	Weak transcription	HSMMtube	muscle
29	chr7:65541800-65556800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr7:65541800-65564600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr7:65541800-65564600	Weak transcription	Fetal Brain Female	brain
32	chr7:65541800-65564800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr7:65542000-65542400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr7:65542000-65542400	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr7:65542000-65542400	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr7:65542000-65542400	Enhancers	Osteobl	bone
37	chr7:65542000-65542600	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr7:65542000-65542600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr7:65542000-65542800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr7:65542000-65542800	Weak transcription	Fetal Stomach	stomach
41	chr7:65542000-65542800	Weak transcription	Lung	lung
42	chr7:65542000-65543000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr7:65542000-65543000	Enhancers	Adipose Nuclei	Adipose
44	chr7:65542000-65543000	Enhancers	NHDF-Ad	bronchial
45	chr7:65542000-65543200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr7:65542000-65543200	Weak transcription	Placenta	Placenta
47	chr7:65542000-65543200	Enhancers	Gastric	stomach
48	chr7:65542000-65543200	Enhancers	Ovary	ovary
49	chr7:65542000-65543600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr7:65542000-65543600	Enhancers	Right Ventricle	heart

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