Variant report

Variant	rs62466625
Chromosome Location	chr7:66497145-66497146
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs12530524	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12530887	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12532208	1.00[AFR][1000 genomes]
rs12532995	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12534156	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12534327	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12535023	0.83[EUR][1000 genomes]
rs12536147	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12536460	1.00[AFR][1000 genomes]
rs12537353	0.83[EUR][1000 genomes]
rs12537633	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12538054	1.00[AFR][1000 genomes]
rs12538144	1.00[AFR][1000 genomes]
rs12538152	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12538350	0.80[EUR][1000 genomes]
rs12538724	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12539202	0.85[EUR][1000 genomes]
rs12539604	0.97[ASN][1000 genomes]
rs12540025	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs28867847	0.94[ASN][1000 genomes]
rs4717335	0.85[ASN][1000 genomes]
rs4717342	0.86[EUR][1000 genomes]
rs4718438	0.91[ASN][1000 genomes]
rs62464960	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62464964	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62464966	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs62464967	0.83[EUR][1000 genomes]
rs62464968	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs62464972	1.00[AFR][1000 genomes]
rs62464974	1.00[AFR][1000 genomes]
rs62464975	1.00[AFR][1000 genomes]
rs62464976	1.00[AFR][1000 genomes]
rs62464977	1.00[AFR][1000 genomes]
rs62466589	0.81[ASN][1000 genomes]
rs62466591	0.97[ASN][1000 genomes]
rs62466592	0.97[ASN][1000 genomes]
rs62466594	0.97[ASN][1000 genomes]
rs62466596	0.97[ASN][1000 genomes]
rs62466612	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62466613	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62466616	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62466618	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62466620	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62466629	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62466630	0.83[EUR][1000 genomes]
rs62468371	0.85[EUR][1000 genomes]
rs62468374	0.88[EUR][1000 genomes]
rs62468375	0.88[EUR][1000 genomes]
rs62468378	0.88[EUR][1000 genomes]
rs62468379	0.88[EUR][1000 genomes]
rs62468380	0.88[EUR][1000 genomes]
rs62468381	0.83[EUR][1000 genomes]
rs62468382	0.83[EUR][1000 genomes]
rs62468403	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1032575	chr7:66432853-66576034	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv981515	chr7:66477535-66532313	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	nsv824151	chr7:66494072-66508524	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv33653	chr7:66494301-66508342	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62466625	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66462400-66500200	Weak transcription	Psoas Muscle	Psoas
2	chr7:66462400-66508000	Weak transcription	Stomach Mucosa	stomach
3	chr7:66462600-66497200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr7:66463000-66507800	Weak transcription	Fetal Brain Male	brain
5	chr7:66463200-66510000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr7:66477000-66499000	Weak transcription	Colonic Mucosa	Colon
7	chr7:66483400-66502000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr7:66483400-66551200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr7:66483600-66534400	Weak transcription	Aorta	Aorta
10	chr7:66485800-66501000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr7:66486400-66531600	Weak transcription	Ovary	ovary
12	chr7:66486600-66507600	Weak transcription	Colon Smooth Muscle	Colon
13	chr7:66487000-66515800	Weak transcription	Fetal Brain Female	brain
14	chr7:66487000-66576600	Weak transcription	Gastric	stomach
15	chr7:66487800-66508600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr7:66488000-66497200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr7:66488000-66500200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr7:66488000-66501000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr7:66488000-66501000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr7:66488000-66501400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr7:66488000-66501400	Weak transcription	Hela-S3	cervix
22	chr7:66488000-66502000	Weak transcription	Brain Angular Gyrus	brain
23	chr7:66488000-66508600	Weak transcription	Fetal Lung	lung
24	chr7:66488000-66511800	Weak transcription	HepG2	liver
25	chr7:66488400-66501000	Weak transcription	Brain Anterior Caudate	brain
26	chr7:66488400-66501800	Weak transcription	Fetal Heart	heart
27	chr7:66488800-66500200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr7:66489200-66498000	Weak transcription	Placenta	Placenta
29	chr7:66490800-66505600	Weak transcription	Small Intestine	intestine
30	chr7:66491000-66501400	Weak transcription	HSMM	muscle
31	chr7:66491000-66507600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:66491200-66500800	Weak transcription	HSMMtube	muscle
33	chr7:66491200-66506000	Weak transcription	Osteobl	bone
34	chr7:66493600-66506000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr7:66495000-66497200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr7:66495000-66501200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr7:66495000-66502000	Weak transcription	Left Ventricle	heart
38	chr7:66495000-66532200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr7:66495200-66497200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr7:66495200-66497200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr7:66495200-66497200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr7:66495200-66497200	Weak transcription	Lung	lung
43	chr7:66495200-66498000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr7:66495200-66498000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr7:66495200-66498000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr7:66495200-66498200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr7:66495200-66498200	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr7:66495200-66498200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr7:66495200-66500800	Weak transcription	Brain Hippocampus Middle	brain
50	chr7:66495200-66506000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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