Variant report

Variant	rs62467444
Chromosome Location	chr7:65572661-65572662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:65571184..65573895-chr7:65578439..65580502,3	K562	blood:
2	chr7:65571049..65574074-chr7:65578628..65580539,3	MCF-7	breast:
3	chr7:65570488..65573331-chr7:65578216..65581893,3	K562	blood:
4	chr7:65563372..65566895-chr7:65568965..65573405,4	MCF-7	breast:
5	chr7:65569097..65570698-chr7:65571096..65573038,2	MCF-7	breast:
6	chr7:65567522..65569449-chr7:65572493..65575376,3	K562	blood:
7	chr7:65566517..65569449-chr7:65571661..65573993,2	K562	blood:

Variant related genes	Relation type
ENSG00000241258	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12530898	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12531358	1.00[AMR][1000 genomes]
rs12532327	1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12534109	0.84[ASN][1000 genomes]
rs12535985	0.84[ASN][1000 genomes]
rs12536292	0.93[AMR][1000 genomes]
rs12537407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537936	0.84[ASN][1000 genomes]
rs12538025	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12540888	0.81[ASN][1000 genomes]
rs2292936	0.84[ASN][1000 genomes]
rs2292937	0.84[ASN][1000 genomes]
rs62465474	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465475	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465476	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465483	0.81[ASN][1000 genomes]
rs62465484	0.86[ASN][1000 genomes]
rs62465512	0.85[AMR][1000 genomes]
rs62465513	0.85[AMR][1000 genomes]
rs62465515	0.85[AMR][1000 genomes]
rs62465542	0.81[ASN][1000 genomes]
rs62467421	1.00[AMR][1000 genomes]
rs62467436	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62467437	1.00[AMR][1000 genomes]
rs62467441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62467442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62467450	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv888325	chr7:65474919-65575893	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1021186	chr7:65492601-65663438	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62467444	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65565200-65579800	Weak transcription	Spleen	Spleen
2	chr7:65565600-65573400	Weak transcription	HepG2	liver
3	chr7:65565600-65575200	Weak transcription	Liver	Liver
4	chr7:65565600-65575800	Weak transcription	HMEC	breast
5	chr7:65565600-65575800	Weak transcription	NH-A	brain
6	chr7:65565600-65579200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr7:65565800-65579000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr7:65565800-65579000	Weak transcription	Brain Hippocampus Middle	brain
9	chr7:65565800-65579000	Weak transcription	Fetal Stomach	stomach
10	chr7:65565800-65579400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr7:65566000-65579000	Weak transcription	Primary T cells from cord blood	blood
12	chr7:65566200-65575800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:65566200-65579000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr7:65566200-65579000	Weak transcription	Brain Substantia Nigra	brain
15	chr7:65566200-65579000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr7:65566200-65579200	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr7:65568200-65573800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:65569200-65575600	Weak transcription	NHEK	skin
19	chr7:65569400-65575800	Weak transcription	A549	lung
20	chr7:65570200-65573800	Enhancers	Hela-S3	cervix
21	chr7:65570400-65572800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr7:65571400-65572800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr7:65571400-65572800	Enhancers	K562	blood
24	chr7:65571400-65575800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr7:65571600-65572800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr7:65571600-65575800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr7:65571800-65575800	Weak transcription	Osteobl	bone
28	chr7:65571800-65576000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr7:65572000-65575800	Weak transcription	NHLF	lung
30	chr7:65572000-65579000	Weak transcription	Brain Angular Gyrus	brain
31	chr7:65572400-65572800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr7:65572400-65575400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr7:65572600-65575000	Weak transcription	Fetal Intestine Small	intestine
34	chr7:65572600-65575200	Weak transcription	NHDF-Ad	bronchial
35	chr7:65572600-65575800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr7:65572600-65576200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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