Variant report

Variant	rs62466638
Chromosome Location	chr7:66528739-66528740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs12530524	0.85[EUR][1000 genomes]
rs12530887	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12531516	0.87[AMR][1000 genomes]
rs12532160	0.87[AMR][1000 genomes]
rs12532208	0.93[AMR][1000 genomes]
rs12532995	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12534156	0.80[EUR][1000 genomes]
rs12534278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12534327	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12535023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12536147	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12537353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12537414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12537633	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12537825	0.81[AMR][1000 genomes]
rs12538152	0.80[EUR][1000 genomes]
rs12538350	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12539202	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12539604	0.81[AMR][1000 genomes]
rs12540025	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12540695	0.87[AMR][1000 genomes]
rs2901442	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs35448884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4717335	0.81[AMR][1000 genomes]
rs4718438	0.81[AMR][1000 genomes]
rs4718450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62464960	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62464964	0.88[EUR][1000 genomes]
rs62464966	0.85[EUR][1000 genomes]
rs62464967	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62464968	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62466582	0.87[AMR][1000 genomes]
rs62466584	0.87[AMR][1000 genomes]
rs62466586	0.87[AMR][1000 genomes]
rs62466588	0.87[AMR][1000 genomes]
rs62466589	0.87[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]
rs62466612	0.80[EUR][1000 genomes]
rs62466613	0.80[EUR][1000 genomes]
rs62466616	0.80[EUR][1000 genomes]
rs62466629	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62466630	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62466632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62466633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62466634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62466635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62466637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62466639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62466640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62466642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62466657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62466659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62468371	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs62468374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62468375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62468378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62468379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62468380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62468381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62468382	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62468385	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62468386	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62468402	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62468403	0.83[EUR][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	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
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62466638	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66483400-66551200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr7:66483600-66534400	Weak transcription	Aorta	Aorta
3	chr7:66486400-66531600	Weak transcription	Ovary	ovary
4	chr7:66487000-66576600	Weak transcription	Gastric	stomach
5	chr7:66495000-66532200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr7:66495200-66538000	Weak transcription	Brain Germinal Matrix	brain
7	chr7:66495200-66539400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr7:66495200-66597200	Weak transcription	Right Ventricle	heart
9	chr7:66495400-66529600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr7:66495400-66531800	Weak transcription	Fetal Kidney	kidney
11	chr7:66495400-66533200	Weak transcription	Thymus	Thymus
12	chr7:66495400-66534400	Weak transcription	Spleen	Spleen
13	chr7:66495600-66532200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:66495600-66533200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr7:66495600-66547400	Weak transcription	Pancreas	Pancrea
16	chr7:66498600-66534600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr7:66498600-66549400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr7:66501000-66540000	Weak transcription	Psoas Muscle	Psoas
19	chr7:66502400-66534400	Weak transcription	Lung	lung
20	chr7:66502400-66549600	Weak transcription	Brain Hippocampus Middle	brain
21	chr7:66506600-66534600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr7:66508000-66532200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr7:66508000-66533400	Weak transcription	Colon Smooth Muscle	Colon
24	chr7:66508800-66528800	Weak transcription	Brain Anterior Caudate	brain
25	chr7:66508800-66533400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr7:66508800-66533800	Weak transcription	Hela-S3	cervix
27	chr7:66508800-66537600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr7:66508800-66538000	Weak transcription	A549	lung
29	chr7:66508800-66590400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr7:66509000-66531200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr7:66509000-66531200	Weak transcription	Osteobl	bone
32	chr7:66509000-66533200	Weak transcription	HSMM	muscle
33	chr7:66509000-66538000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr7:66509000-66539600	Weak transcription	HMEC	breast
35	chr7:66509400-66533000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr7:66509400-66536600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr7:66510800-66532000	Weak transcription	K562	blood
38	chr7:66511200-66537600	Weak transcription	Brain Substantia Nigra	brain
39	chr7:66511400-66539800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr7:66512000-66529200	Weak transcription	Primary B cells from cord blood	blood
41	chr7:66512000-66531600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr7:66512400-66535000	Weak transcription	Colonic Mucosa	Colon
43	chr7:66512400-66540600	Weak transcription	HepG2	liver
44	chr7:66515600-66537600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr7:66515600-66538000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr7:66516200-66534400	Weak transcription	Placenta	Placenta
47	chr7:66516400-66533000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr7:66516400-66534600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr7:66516400-66551600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr7:66516600-66533200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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