Variant report

Variant	rs62465748
Chromosome Location	chr7:66370250-66370251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10499785	0.85[ASN][1000 genomes]
rs12531377	0.85[ASN][1000 genomes]
rs12531516	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532160	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12532307	0.82[EUR][1000 genomes]
rs12532650	0.81[AMR][1000 genomes]
rs12532888	0.85[ASN][1000 genomes]
rs12533830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12533958	0.85[ASN][1000 genomes]
rs12534401	0.85[ASN][1000 genomes]
rs12535268	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12536130	0.85[ASN][1000 genomes]
rs12537825	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12537955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12538126	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12539366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539848	0.85[ASN][1000 genomes]
rs12540312	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12540447	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12540695	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17567255	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2091314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34758320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35279320	0.85[ASN][1000 genomes]
rs3735153	0.85[ASN][1000 genomes]
rs3778911	0.85[ASN][1000 genomes]
rs3800819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4717323	0.81[AMR][1000 genomes]
rs4717324	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4717329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4717332	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4718407	0.85[ASN][1000 genomes]
rs4718409	0.85[ASN][1000 genomes]
rs4718426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4718434	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62464646	0.85[ASN][1000 genomes]
rs62464647	0.85[ASN][1000 genomes]
rs62464648	0.85[ASN][1000 genomes]
rs62464651	0.85[ASN][1000 genomes]
rs62464652	0.85[ASN][1000 genomes]
rs62464653	0.85[ASN][1000 genomes]
rs62464654	0.85[ASN][1000 genomes]
rs62464655	0.85[ASN][1000 genomes]
rs62464658	0.85[ASN][1000 genomes]
rs62464659	0.85[ASN][1000 genomes]
rs62465676	0.85[ASN][1000 genomes]
rs62465678	0.85[ASN][1000 genomes]
rs62465681	0.85[ASN][1000 genomes]
rs62465682	0.85[ASN][1000 genomes]
rs62465688	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465698	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465699	0.87[AMR][1000 genomes]
rs62465700	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465701	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465705	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465706	0.87[AMR][1000 genomes]
rs62465707	0.87[AMR][1000 genomes]
rs62465709	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465710	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62465712	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62465713	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62465714	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62465716	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62465730	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62465734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62465736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465742	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62466575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62466578	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62466582	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62466584	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62466586	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62466588	0.87[AMR][1000 genomes]
rs62466589	0.87[AMR][1000 genomes]
rs62468261	0.85[ASN][1000 genomes]
rs62468262	0.85[ASN][1000 genomes]
rs62468263	0.85[ASN][1000 genomes]
rs7781008	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
2	nsv888329	chr7:66234585-66376095	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62465748	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66311000-66385200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr7:66311200-66385200	Weak transcription	Brain Angular Gyrus	brain
3	chr7:66325600-66373000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr7:66326400-66371800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr7:66329800-66372000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr7:66331800-66378400	Weak transcription	A549	lung
7	chr7:66333000-66371600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr7:66333800-66371800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr7:66335400-66371400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr7:66342800-66370600	Weak transcription	NHLF	lung
11	chr7:66350600-66385200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:66353200-66379600	Weak transcription	GM12878-XiMat	blood
13	chr7:66355600-66375400	Weak transcription	Fetal Brain Male	brain
14	chr7:66356400-66371200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr7:66358800-66371200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr7:66359200-66372800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr7:66361200-66372600	Weak transcription	Osteobl	bone
18	chr7:66361400-66371000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr7:66361600-66370400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr7:66362600-66371000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr7:66362600-66371200	Strong transcription	Fetal Intestine Small	intestine
22	chr7:66363000-66371800	Strong transcription	Fetal Stomach	stomach
23	chr7:66363200-66371200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr7:66363200-66373000	Weak transcription	Right Atrium	heart
25	chr7:66364000-66371000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr7:66364000-66375600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:66364400-66370400	Strong transcription	Placenta Amnion	Placenta Amnion
28	chr7:66364400-66385400	Weak transcription	HSMMtube	muscle
29	chr7:66364600-66371800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr7:66364600-66372600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr7:66364800-66371800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr7:66364800-66372400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr7:66364800-66378400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr7:66364800-66385000	Weak transcription	Brain Anterior Caudate	brain
35	chr7:66365000-66373400	Weak transcription	Primary B cells from peripheral blood	blood
36	chr7:66366000-66371800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr7:66366000-66371800	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr7:66366400-66385600	Weak transcription	Brain Substantia Nigra	brain
39	chr7:66366600-66374200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr7:66366800-66372600	Weak transcription	K562	blood
41	chr7:66366800-66375800	Weak transcription	HepG2	liver
42	chr7:66366800-66378800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:66367400-66371600	Weak transcription	Gastric	stomach
44	chr7:66367400-66373800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr7:66367600-66372800	Weak transcription	Liver	Liver
46	chr7:66367600-66375600	Weak transcription	Lung	lung
47	chr7:66368000-66371400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr7:66368000-66372600	Weak transcription	Spleen	Spleen
49	chr7:66368000-66373200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr7:66368000-66385400	Weak transcription	Adipose Nuclei	Adipose

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