Variant report

Variant	rs62470880
Chromosome Location	chr7:65339203-65339204
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65214366..65217502-chr7:65337041..65339664,3	MCF-7	breast:
2	chr7:65337864..65339398-chr7:65445758..65448693,2	K562	blood:

Variant related genes	Relation type
ENSG00000169919	Chromatin interaction
ENSG00000228409	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs12530898	1.00[AFR][1000 genomes]
rs12532327	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2279904	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35832738	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs3735141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62467382	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62467384	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62467385	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62467386	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62467387	0.90[EUR][1000 genomes]
rs62467410	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62467411	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62467413	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62467414	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62467421	1.00[AFR][1000 genomes]
rs62467437	1.00[AFR][1000 genomes]
rs62469938	0.82[EUR][1000 genomes]
rs62469939	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62469940	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62470862	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62470863	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62470864	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62470868	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62470870	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62470879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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];0.90[ASN][1000 genomes]
rs62470895	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][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]
rs62470922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62470924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62470925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62470926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62470931	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62470932	0.82[EUR][1000 genomes]
rs62470934	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62470938	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62470940	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62470944	0.90[EUR][1000 genomes]
rs62470945	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	esv3339156	chr7:64510176-65349050	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv2759534	chr7:64551274-65373851	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv427788	chr7:64551274-65390424	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv2764020	chr7:64594065-65351820	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv1029942	chr7:64679680-65371565	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv538903	chr7:64679680-65371565	Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv1019667	chr7:64679680-65380603	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
9	esv2757227	chr7:64694241-65373851	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
10	nsv1025207	chr7:65092426-65339879	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv1033400	chr7:65092426-65339879	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
12	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
13	nsv1020622	chr7:65161364-65339879	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv1029800	chr7:65309327-65367692	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	esv3427026	chr7:65336942-65339890	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
16	esv3414148	chr7:65337017-65339740	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62470880	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65337400-65339600	Active TSS	A549	lung
2	chr7:65337600-65339400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:65337600-65339400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:65337600-65339400	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr7:65337600-65339400	Active TSS	Fetal Thymus	thymus
6	chr7:65337600-65339400	Active TSS	Ovary	ovary
7	chr7:65337600-65339400	Active TSS	Thymus	Thymus
8	chr7:65337600-65339600	Active TSS	H9 Cell Line	embryonic stem cell
9	chr7:65337600-65339600	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr7:65337600-65339600	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr7:65337600-65339600	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr7:65337600-65339600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr7:65337600-65339600	Active TSS	Brain Angular Gyrus	brain
14	chr7:65337600-65339600	Active TSS	Brain Anterior Caudate	brain
15	chr7:65337600-65339600	Active TSS	Brain Cingulate Gyrus	brain
16	chr7:65337600-65339600	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr7:65337600-65339600	Active TSS	HMEC	breast
18	chr7:65337600-65340000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr7:65337600-65340000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr7:65337800-65339400	Active TSS	H1 Cell Line	embryonic stem cell
21	chr7:65337800-65339600	Active TSS	Brain Germinal Matrix	brain
22	chr7:65338000-65339400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr7:65338000-65339400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr7:65338000-65339400	Active TSS	Psoas Muscle	Psoas
25	chr7:65338000-65339600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr7:65338200-65339400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr7:65338200-65339400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr7:65338200-65339400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr7:65338200-65339400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr7:65338200-65339400	Active TSS	Aorta	Aorta
31	chr7:65338200-65339400	Active TSS	Esophagus	oesophagus
32	chr7:65338200-65339400	Active TSS	Fetal Intestine Large	intestine
33	chr7:65338200-65339400	Active TSS	Fetal Intestine Small	intestine
34	chr7:65338200-65339400	Active TSS	Left Ventricle	heart
35	chr7:65338200-65339400	Active TSS	Lung	lung
36	chr7:65338200-65339400	Active TSS	Pancreas	Pancrea
37	chr7:65338200-65339400	Active TSS	Right Atrium	heart
38	chr7:65338200-65339400	Active TSS	Stomach Smooth Muscle	stomach
39	chr7:65338200-65339400	Active TSS	HSMM	muscle
40	chr7:65338200-65339600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr7:65338200-65339600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr7:65338200-65339600	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr7:65338200-65339600	Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr7:65338200-65339600	Active TSS	Muscle Satellite Cultured Cells	--
45	chr7:65338200-65339600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr7:65338200-65339600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr7:65338200-65339600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr7:65338200-65339600	Active TSS	Colonic Mucosa	Colon
49	chr7:65338200-65339600	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr7:65338200-65339600	Active TSS	Fetal Stomach	stomach

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