Variant report

Variant	rs62470925
Chromosome Location	chr7:65414214-65414215
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12530898	1.00[AFR][1000 genomes]
rs12532327	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12534109	1.00[AFR][1000 genomes]
rs12535985	1.00[AFR][1000 genomes]
rs12537936	1.00[AFR][1000 genomes]
rs12538025	1.00[AFR][1000 genomes]
rs2279904	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2292936	1.00[AFR][1000 genomes]
rs2292937	1.00[AFR][1000 genomes]
rs35832738	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3735141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465474	1.00[AFR][1000 genomes]
rs62465475	1.00[AFR][1000 genomes]
rs62465476	1.00[AFR][1000 genomes]
rs62465483	1.00[AFR][1000 genomes]
rs62465484	1.00[AFR][1000 genomes]
rs62467382	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62467384	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62467385	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62467386	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62467387	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62467410	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62467411	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62467413	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62467414	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62467421	1.00[AFR][1000 genomes]
rs62467437	1.00[AFR][1000 genomes]
rs62467450	1.00[AFR][1000 genomes]
rs62469938	0.82[EUR][1000 genomes]
rs62469939	0.87[EUR][1000 genomes]
rs62469940	0.87[EUR][1000 genomes]
rs62470862	0.87[EUR][1000 genomes]
rs62470863	0.87[EUR][1000 genomes]
rs62470864	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62470868	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62470870	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62470879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62470880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62470883	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62470884	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62470886	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62470891	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62470894	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62470895	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62470897	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62470899	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62470900	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62470921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62470922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62470924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62470926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62470931	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62470932	0.82[EUR][1000 genomes]
rs62470934	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62470938	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62470940	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62470944	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62470945	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429767	chr7:64473713-65415647	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv1020337	chr7:65371505-65449654	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
5	nsv1025494	chr7:65402301-65515606	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv538906	chr7:65402301-65515606	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv888321	chr7:65408904-65449541	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	esv9823	chr7:65413362-65468020	Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	esv3426468	chr7:65413488-65462982	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
10	esv3433491	chr7:65414034-65463477	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
11	nsv1028971	chr7:65414064-65457437	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62470925	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65345200-65419000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr7:65368800-65418800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr7:65368800-65419000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:65373800-65424000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:65375000-65418800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr7:65375600-65419800	Weak transcription	HSMMtube	muscle
7	chr7:65379200-65419000	Weak transcription	Fetal Thymus	thymus
8	chr7:65381800-65420200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr7:65382000-65420600	Weak transcription	Primary B cells from cord blood	blood
10	chr7:65382800-65419800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr7:65383200-65419000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr7:65383800-65419600	Weak transcription	GM12878-XiMat	blood
13	chr7:65389400-65423800	Weak transcription	Aorta	Aorta
14	chr7:65390400-65419000	Weak transcription	Thymus	Thymus
15	chr7:65390600-65423800	Weak transcription	Gastric	stomach
16	chr7:65392600-65418400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:65393200-65419600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr7:65393400-65419000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr7:65395600-65420400	Weak transcription	Esophagus	oesophagus
20	chr7:65395800-65420000	Weak transcription	Fetal Lung	lung
21	chr7:65396600-65418600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr7:65396800-65416800	Weak transcription	Hela-S3	cervix
23	chr7:65396800-65420000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr7:65397400-65419600	Weak transcription	Left Ventricle	heart
25	chr7:65399200-65425000	Weak transcription	Small Intestine	intestine
26	chr7:65399800-65419600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr7:65400200-65420200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:65400800-65420200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr7:65401000-65417200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr7:65401200-65420000	Weak transcription	HUVEC	blood vessel
31	chr7:65401200-65423800	Weak transcription	Spleen	Spleen
32	chr7:65401400-65425000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr7:65401800-65425000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr7:65402000-65420200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr7:65402000-65424800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr7:65402000-65425000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr7:65402200-65419000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr7:65402400-65419400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr7:65402800-65417800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr7:65403800-65419000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr7:65403800-65419600	Weak transcription	Osteobl	bone
42	chr7:65404000-65418800	Weak transcription	Fetal Muscle Leg	muscle
43	chr7:65404000-65420400	Weak transcription	HSMM	muscle
44	chr7:65404200-65417800	Weak transcription	Primary T cells from cord blood	blood
45	chr7:65404200-65418400	Weak transcription	K562	blood
46	chr7:65404200-65418800	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr7:65404400-65416800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr7:65404400-65419000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr7:65404400-65419000	Weak transcription	Fetal Muscle Trunk	muscle
50	chr7:65404400-65419000	Weak transcription	Lung	lung

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