Variant report

Variant	rs62466582
Chromosome Location	chr7:66425343-66425344
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:66424885..66426980-chr7:66429795..66432252,2	MCF-7	breast:
2	chr7:66421917..66425693-chr7:66427174..66429869,5	K562	blood:
3	chr7:66411722..66413311-chr7:66423675..66425541,2	K562	blood:
4	chr7:66424823..66427121-chr7:66447406..66450272,2	K562	blood:

Extended variants
information (count: 119 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10499785	0.85[ASN][1000 genomes]
rs12531377	0.85[ASN][1000 genomes]
rs12531516	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532160	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12532307	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12532650	0.81[AMR][1000 genomes]
rs12532888	0.85[ASN][1000 genomes]
rs12533830	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12533958	0.85[ASN][1000 genomes]
rs12534278	0.87[AMR][1000 genomes]
rs12534401	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12535023	0.87[AMR][1000 genomes]
rs12535268	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12536130	0.85[ASN][1000 genomes]
rs12537353	0.87[AMR][1000 genomes]
rs12537414	0.87[AMR][1000 genomes]
rs12537825	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12537955	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12538126	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12539366	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539604	0.81[AMR][1000 genomes]
rs12539848	0.85[ASN][1000 genomes]
rs12540312	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12540447	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12540695	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17567255	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2091314	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293351	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34758320	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35279320	0.85[ASN][1000 genomes]
rs35448884	0.87[AMR][1000 genomes]
rs3735153	0.85[ASN][1000 genomes]
rs3778911	0.85[ASN][1000 genomes]
rs3800819	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4717323	0.81[AMR][1000 genomes]
rs4717324	0.85[ASN][1000 genomes]
rs4717329	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4717332	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4717335	0.81[AMR][1000 genomes]
rs4718407	0.85[ASN][1000 genomes]
rs4718409	0.85[ASN][1000 genomes]
rs4718426	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4718434	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4718438	0.81[AMR][1000 genomes]
rs4718450	0.87[AMR][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	0.85[ASN][1000 genomes]
rs62465698	0.85[ASN][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]
rs62465709	0.85[ASN][1000 genomes]
rs62465710	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62465712	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62465713	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62465714	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62465716	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62465730	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62465734	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465736	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465738	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465739	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465740	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465741	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465742	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465743	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465744	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465745	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465747	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465748	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465750	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465752	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62466575	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62466578	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62466584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62466586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62466588	1.00[AMR][1000 genomes]
rs62466589	1.00[AMR][1000 genomes]
rs62466591	0.81[AMR][1000 genomes]
rs62466592	0.81[AMR][1000 genomes]
rs62466594	0.81[AMR][1000 genomes]
rs62466596	0.81[AMR][1000 genomes]
rs62466632	0.87[AMR][1000 genomes]
rs62466633	0.87[AMR][1000 genomes]
rs62466634	0.87[AMR][1000 genomes]
rs62466635	0.87[AMR][1000 genomes]
rs62466637	0.87[AMR][1000 genomes]
rs62466638	0.87[AMR][1000 genomes]
rs62466639	0.87[AMR][1000 genomes]
rs62466640	0.87[AMR][1000 genomes]
rs62466642	0.87[AMR][1000 genomes]
rs62466657	0.87[AMR][1000 genomes]
rs62466659	0.87[AMR][1000 genomes]
rs62468261	0.85[ASN][1000 genomes]
rs62468262	0.85[ASN][1000 genomes]
rs62468263	0.85[ASN][1000 genomes]
rs62468374	0.87[AMR][1000 genomes]
rs62468375	0.87[AMR][1000 genomes]
rs62468378	0.87[AMR][1000 genomes]
rs62468379	0.87[AMR][1000 genomes]
rs62468380	0.87[AMR][1000 genomes]
rs62468381	0.87[AMR][1000 genomes]
rs62468382	0.87[AMR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62466582	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	chr7:66387600-66428000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:66400600-66426400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr7:66403400-66426000	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr7:66403400-66426400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr7:66403600-66425600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr7:66403600-66426400	Strong transcription	Thymus	Thymus
7	chr7:66403600-66426600	Strong transcription	Fetal Stomach	stomach
8	chr7:66403800-66425800	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr7:66406000-66426400	Strong transcription	Fetal Thymus	thymus
10	chr7:66406600-66425800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:66406600-66425800	Strong transcription	Liver	Liver
12	chr7:66406600-66425800	Strong transcription	Fetal Brain Female	brain
13	chr7:66406600-66426400	Strong transcription	Fetal Muscle Trunk	muscle
14	chr7:66406800-66425800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr7:66406800-66425800	Strong transcription	Adipose Nuclei	Adipose
16	chr7:66406800-66426000	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr7:66406800-66426000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr7:66409400-66425800	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr7:66409800-66425800	Strong transcription	Brain Germinal Matrix	brain
20	chr7:66411400-66425400	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr7:66417400-66425800	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr7:66417800-66425800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr7:66418000-66425800	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr7:66418000-66425800	Strong transcription	Lung	lung
25	chr7:66418000-66426600	Strong transcription	Spleen	Spleen
26	chr7:66418000-66427000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr7:66418200-66425800	Strong transcription	Placenta	Placenta
28	chr7:66418200-66426400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr7:66418200-66426400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr7:66418200-66426600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr7:66418200-66426800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr7:66418400-66426200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr7:66418400-66426400	Weak transcription	Small Intestine	intestine
34	chr7:66418400-66427200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr7:66418800-66426400	Strong transcription	A549	lung
36	chr7:66420600-66459200	Weak transcription	Psoas Muscle	Psoas
37	chr7:66421000-66425600	Weak transcription	Aorta	Aorta
38	chr7:66421000-66427200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr7:66421400-66428000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr7:66421400-66429200	Weak transcription	Fetal Brain Male	brain
41	chr7:66421400-66435200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr7:66422000-66427000	Strong transcription	NHLF	lung
43	chr7:66422400-66425600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr7:66422600-66426400	Strong transcription	Esophagus	oesophagus
45	chr7:66422600-66430400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr7:66422800-66425800	Strong transcription	Gastric	stomach
47	chr7:66422800-66425800	Strong transcription	Pancreas	Pancrea
48	chr7:66422800-66427000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr7:66422800-66428200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr7:66423200-66425800	Strong transcription	Right Ventricle	heart

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