Variant report

Variant	rs62465547
Chromosome Location	chr7:65683622-65683623
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:65683570-65683716	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr7:65683573-65683731	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:65603533..65606431-chr7:65683250..65685813,2	K562	blood:
2	chr7:65669466..65673274-chr7:65681767..65684284,3	K562	blood:
3	chr7:65676565..65678528-chr7:65683299..65686041,2	MCF-7	breast:

Variant related genes	Relation type
TPST1	TF binding region
ENSG00000169902	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs12530506	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12530746	0.81[EUR][1000 genomes]
rs12530898	1.00[AFR][1000 genomes]
rs12531900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12532247	0.81[EUR][1000 genomes]
rs12532249	0.81[EUR][1000 genomes]
rs12532278	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12532327	1.00[AFR][1000 genomes]
rs12532383	0.81[EUR][1000 genomes]
rs12532423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12532675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12533387	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12534109	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12534249	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12534477	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12534881	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12535985	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12536816	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12537039	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12537368	0.81[EUR][1000 genomes]
rs12537698	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12537936	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12538025	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12538147	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12538379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12538961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12540888	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1363056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2292936	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2292937	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35832738	1.00[AFR][1000 genomes]
rs35910256	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3735145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3815684	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4149467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4717291	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4718342	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4718345	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4718350	0.81[EUR][1000 genomes]
rs62465362	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62465363	0.87[AMR][1000 genomes]
rs62465364	0.87[AMR][1000 genomes]
rs62465365	0.87[AMR][1000 genomes]
rs62465367	0.87[AMR][1000 genomes]
rs62465372	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62465373	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62465376	1.00[AMR][1000 genomes]
rs62465377	0.93[AMR][1000 genomes]
rs62465380	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62465389	0.81[EUR][1000 genomes]
rs62465392	0.81[EUR][1000 genomes]
rs62465394	0.81[EUR][1000 genomes]
rs62465395	0.81[EUR][1000 genomes]
rs62465396	0.81[EUR][1000 genomes]
rs62465397	0.81[EUR][1000 genomes]
rs62465474	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs62465475	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs62465476	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs62465483	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62465484	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62465512	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465513	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465515	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465519	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465521	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465522	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465525	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465526	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465527	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465542	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62465546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62465554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62467382	1.00[AFR][1000 genomes]
rs62467384	1.00[AFR][1000 genomes]
rs62467385	1.00[AFR][1000 genomes]
rs62467386	1.00[AFR][1000 genomes]
rs62467410	1.00[AFR][1000 genomes]
rs62467411	1.00[AFR][1000 genomes]
rs62467413	1.00[AFR][1000 genomes]
rs62467414	1.00[AFR][1000 genomes]
rs62467421	1.00[AFR][1000 genomes]
rs62467437	1.00[AFR][1000 genomes]
rs62467450	1.00[AFR][1000 genomes]
rs62468669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62468673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62468674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62468677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62468679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62468696	0.81[EUR][1000 genomes]
rs62468699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62468700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62468702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62468705	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62468707	0.87[AMR][1000 genomes]
rs62468708	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs62468711	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62468712	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62470940	1.00[AFR][1000 genomes]
rs62470945	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv1028692	chr7:65673136-65751069	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv538908	chr7:65673136-65751069	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62465547	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65671600-65685400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:65671600-65689000	Weak transcription	Pancreas	Pancrea
3	chr7:65672200-65687400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:65672200-65723400	Weak transcription	Right Atrium	heart
5	chr7:65672600-65687600	Weak transcription	Brain Germinal Matrix	brain
6	chr7:65673000-65689000	Weak transcription	HMEC	breast
7	chr7:65673400-65689000	Weak transcription	Brain Hippocampus Middle	brain
8	chr7:65674000-65688800	Weak transcription	Ovary	ovary
9	chr7:65675600-65685400	Weak transcription	Esophagus	oesophagus
10	chr7:65676000-65684400	Weak transcription	HepG2	liver
11	chr7:65676000-65689000	Weak transcription	Lung	lung
12	chr7:65676000-65696200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr7:65676000-65716800	Weak transcription	Primary B cells from cord blood	blood
14	chr7:65676200-65696200	Weak transcription	Fetal Stomach	stomach
15	chr7:65676600-65691200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:65676600-65693200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:65676800-65685400	Weak transcription	Gastric	stomach
18	chr7:65677000-65694600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr7:65677200-65693800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:65677800-65688800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr7:65679200-65684200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr7:65679200-65685400	Weak transcription	NHDF-Ad	bronchial
23	chr7:65679200-65686200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr7:65679200-65686200	Weak transcription	Osteobl	bone
25	chr7:65679200-65686600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr7:65679200-65686600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr7:65679200-65687600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr7:65679200-65688600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr7:65682400-65684200	Weak transcription	Liver	Liver
30	chr7:65683200-65685200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr7:65683600-65684000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:65683600-65684200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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