Variant report

Variant	rs62468385
Chromosome Location	chr7:66586482-66586483
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1128730	0.87[ASN][1000 genomes]
rs12530524	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12530887	0.80[EUR][1000 genomes]
rs12532208	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12532995	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12534156	0.80[EUR][1000 genomes]
rs12534278	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12534327	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12535023	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12535931	0.83[AMR][1000 genomes]
rs12536147	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12537353	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12537414	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12537633	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12538054	0.83[ASN][1000 genomes]
rs12538144	0.83[ASN][1000 genomes]
rs12538152	0.80[EUR][1000 genomes]
rs12538350	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12539202	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12540025	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2901442	1.00[AFR][1000 genomes]
rs35448884	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4718450	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62464960	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62464964	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62464966	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62464967	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62464968	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62464974	0.86[ASN][1000 genomes]
rs62464975	0.86[ASN][1000 genomes]
rs62464976	0.86[ASN][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];0.82[EUR][1000 genomes]
rs62466630	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62466632	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62466633	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62466634	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62466635	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62466637	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62466638	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62466639	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62466640	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62466642	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62466657	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62466659	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62468371	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62468374	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62468375	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62468378	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62468379	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62468380	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62468381	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62468382	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62468386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62468402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62468403	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv966838	chr7:66548076-66617503	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
6	esv1802655	chr7:66576034-66634666	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
7	esv1816643	chr7:66576034-66634666	Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
8	esv1840497	chr7:66576034-66634666	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
9	esv1851064	chr7:66576034-66634666	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62468385	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66495200-66597200	Weak transcription	Right Ventricle	heart
2	chr7:66508800-66590400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr7:66532400-66587600	Weak transcription	Fetal Kidney	kidney
4	chr7:66533800-66623200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr7:66535600-66593600	Weak transcription	Hela-S3	cervix
6	chr7:66538400-66593600	Weak transcription	Fetal Thymus	thymus
7	chr7:66538400-66594200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:66538400-66595800	Weak transcription	Brain Substantia Nigra	brain
9	chr7:66540800-66594000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr7:66543400-66600000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:66544600-66592600	Weak transcription	HepG2	liver
12	chr7:66545600-66616600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr7:66547000-66594200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr7:66547600-66594000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr7:66547600-66594000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:66547800-66593400	Weak transcription	Pancreas	Pancrea
17	chr7:66547800-66602800	Weak transcription	Fetal Muscle Leg	muscle
18	chr7:66550000-66587800	Weak transcription	Brain Hippocampus Middle	brain
19	chr7:66550000-66593400	Weak transcription	Spleen	Spleen
20	chr7:66550000-66624000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr7:66550200-66593200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr7:66554600-66595000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr7:66555800-66587400	Weak transcription	Primary B cells from cord blood	blood
24	chr7:66560400-66593600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr7:66560800-66589200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr7:66562800-66593600	Weak transcription	NHEK	skin
27	chr7:66564800-66594400	Weak transcription	NH-A	brain
28	chr7:66565200-66589800	Weak transcription	Aorta	Aorta
29	chr7:66566400-66587400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr7:66566400-66587600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr7:66566400-66593400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr7:66566400-66605600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr7:66566600-66593400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr7:66566800-66594000	Weak transcription	Lung	lung
35	chr7:66567000-66593000	Weak transcription	Primary B cells from peripheral blood	blood
36	chr7:66568800-66594200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr7:66570600-66595800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr7:66570800-66591000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr7:66570800-66592800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr7:66570800-66592800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr7:66570800-66593400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr7:66570800-66595400	Weak transcription	Ovary	ovary
43	chr7:66571200-66593400	Weak transcription	Dnd41	blood
44	chr7:66572600-66593400	Weak transcription	Liver	Liver
45	chr7:66575000-66593400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr7:66575600-66593000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr7:66575800-66594000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr7:66576000-66587800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr7:66576000-66600600	Weak transcription	Fetal Lung	lung
50	chr7:66576400-66591000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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