Variant report

Variant	rs62465002
Chromosome Location	chr7:66677731-66677732
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12530782	1.00[AFR][1000 genomes]
rs12537561	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12537954	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17144570	0.82[AMR][1000 genomes]
rs28847740	0.83[EUR][1000 genomes]
rs4717359	0.82[AMR][1000 genomes]
rs4718480	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62464976	0.82[AMR][1000 genomes]
rs62465000	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62465005	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465013	1.00[AFR][1000 genomes]
rs62465014	1.00[AFR][1000 genomes]
rs62465037	0.82[AMR][1000 genomes]
rs62465038	0.82[AMR][1000 genomes]
rs62465040	0.82[AMR][1000 genomes]
rs62465044	0.82[AMR][1000 genomes]
rs62465047	0.81[AMR][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	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	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
6	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62465002	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66628600-66684600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr7:66644400-66683000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr7:66648200-66679800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr7:66649200-66679200	Weak transcription	NHEK	skin
5	chr7:66654400-66681600	Weak transcription	Spleen	Spleen
6	chr7:66654600-66678200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:66654600-66683400	Weak transcription	Pancreas	Pancrea
8	chr7:66654600-66684600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr7:66654600-66704600	Weak transcription	Gastric	stomach
10	chr7:66654600-66709600	Weak transcription	Lung	lung
11	chr7:66658000-66703200	Weak transcription	Ovary	ovary
12	chr7:66658200-66678600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:66658400-66678200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr7:66658600-66678600	Weak transcription	A549	lung
15	chr7:66658600-66679600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr7:66658600-66691000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:66659000-66678200	Weak transcription	Left Ventricle	heart
18	chr7:66660600-66701600	Weak transcription	Fetal Kidney	kidney
19	chr7:66660600-66703000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr7:66662400-66683000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr7:66662600-66679800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:66665200-66686200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr7:66665200-66686800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr7:66665600-66706800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr7:66665800-66703400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:66667800-66738400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr7:66670400-66682800	Weak transcription	Fetal Intestine Small	intestine
28	chr7:66670600-66713800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr7:66672600-66677800	Weak transcription	Primary B cells from cord blood	blood
30	chr7:66672600-66688000	Weak transcription	Primary B cells from peripheral blood	blood
31	chr7:66673600-66678000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr7:66674000-66691400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr7:66675800-66678400	Weak transcription	Fetal Stomach	stomach
34	chr7:66675800-66679400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr7:66675800-66683800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr7:66675800-66693800	Weak transcription	Fetal Lung	lung
37	chr7:66675800-66706600	Weak transcription	Aorta	Aorta
38	chr7:66675800-66706800	Weak transcription	Primary T cells from cord blood	blood
39	chr7:66676000-66677800	Weak transcription	Fetal Brain Male	brain
40	chr7:66676000-66680000	Weak transcription	Adipose Nuclei	Adipose
41	chr7:66676000-66681200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr7:66676000-66684600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr7:66676000-66687800	Weak transcription	Dnd41	blood
44	chr7:66676000-66688000	Weak transcription	HSMM	muscle
45	chr7:66676000-66690200	Weak transcription	K562	blood
46	chr7:66676000-66691000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr7:66676000-66702800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr7:66676200-66679000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr7:66676400-66678200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr7:66676600-66678200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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