Variant report

Variant	rs62468403
Chromosome Location	chr7:66593356-66593357
allele	A/G
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	0.84[ASN][1000 genomes]
rs12530524	1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12530887	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12532208	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12532995	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12534278	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12534327	0.83[EUR][1000 genomes]
rs12535023	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12535931	0.83[EUR][1000 genomes]
rs12536147	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12536460	1.00[AFR][1000 genomes]
rs12537353	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12537414	0.83[EUR][1000 genomes]
rs12537633	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12538054	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12538144	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12538350	0.86[EUR][1000 genomes]
rs12539202	0.85[EUR][1000 genomes]
rs12540025	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35448884	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4718450	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62464960	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62464964	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62464966	1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs62464967	0.91[ASN][1000 genomes]
rs62464968	1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs62464972	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs62464974	1.00[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs62464975	1.00[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs62464976	1.00[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs62464977	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs62466618	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs62466620	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs62466625	1.00[AFR][1000 genomes]
rs62466629	0.83[EUR][1000 genomes]
rs62466630	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62466632	0.83[EUR][1000 genomes]
rs62466633	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62466634	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62466635	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62466637	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62466638	0.83[EUR][1000 genomes]
rs62466639	0.80[EUR][1000 genomes]
rs62466640	0.83[EUR][1000 genomes]
rs62466642	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62466657	0.83[EUR][1000 genomes]
rs62466659	0.83[EUR][1000 genomes]
rs62468371	0.85[EUR][1000 genomes]
rs62468374	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62468375	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62468378	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62468379	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62468380	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62468381	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62468382	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62468385	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62468386	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62468402	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[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
rs62468403	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66495200-66597200	Weak transcription	Right Ventricle	heart
2	chr7:66533800-66623200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr7:66535600-66593600	Weak transcription	Hela-S3	cervix
4	chr7:66538400-66593600	Weak transcription	Fetal Thymus	thymus
5	chr7:66538400-66594200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr7:66538400-66595800	Weak transcription	Brain Substantia Nigra	brain
7	chr7:66540800-66594000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr7:66543400-66600000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:66545600-66616600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr7:66547000-66594200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr7:66547600-66594000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr7:66547600-66594000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr7:66547800-66593400	Weak transcription	Pancreas	Pancrea
14	chr7:66547800-66602800	Weak transcription	Fetal Muscle Leg	muscle
15	chr7:66550000-66593400	Weak transcription	Spleen	Spleen
16	chr7:66550000-66624000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr7:66554600-66595000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:66560400-66593600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:66562800-66593600	Weak transcription	NHEK	skin
20	chr7:66564800-66594400	Weak transcription	NH-A	brain
21	chr7:66566400-66593400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr7:66566400-66605600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr7:66566600-66593400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr7:66566800-66594000	Weak transcription	Lung	lung
25	chr7:66568800-66594200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr7:66570600-66595800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr7:66570800-66593400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr7:66570800-66595400	Weak transcription	Ovary	ovary
29	chr7:66571200-66593400	Weak transcription	Dnd41	blood
30	chr7:66572600-66593400	Weak transcription	Liver	Liver
31	chr7:66575000-66593400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr7:66575800-66594000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr7:66576000-66600600	Weak transcription	Fetal Lung	lung
34	chr7:66576600-66616600	Weak transcription	Fetal Stomach	stomach
35	chr7:66580600-66593400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr7:66582400-66593400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr7:66583200-66593400	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr7:66583200-66593400	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr7:66584200-66594200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr7:66584200-66606600	Weak transcription	HSMMtube	muscle
41	chr7:66584400-66593400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr7:66584400-66595600	Weak transcription	Placenta	Placenta
43	chr7:66584400-66624400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr7:66584600-66593400	Weak transcription	Fetal Intestine Large	intestine
45	chr7:66585000-66595600	Weak transcription	Adipose Nuclei	Adipose
46	chr7:66585000-66622400	Weak transcription	HSMM	muscle
47	chr7:66585000-66623600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr7:66585200-66627200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr7:66585800-66594000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr7:66586000-66594400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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