Variant report

Variant	rs778365
Chromosome Location	chr2:233774828-233774829
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	KAP1	chr2:233774659-233774970	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:233774109..233776065-chr2:233791221..233792997,2	MCF-7	breast:
2	chr2:233772342..233775238-chr2:233775790..233777657,2	K562	blood:

Variant related genes	Relation type
NGEF	TF binding region
ENSG00000066248	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1878287	0.89[EUR][1000 genomes]
rs1980168	0.88[EUR][1000 genomes]
rs1980169	0.88[EUR][1000 genomes]
rs1996342	0.88[EUR][1000 genomes]
rs2102788	0.88[EUR][1000 genomes]
rs2592120	0.94[EUR][1000 genomes]
rs2675959	0.90[EUR][1000 genomes]
rs2675964	0.93[EUR][1000 genomes]
rs2675965	0.93[EUR][1000 genomes]
rs2921705	0.88[EUR][1000 genomes]
rs2944591	0.91[EUR][1000 genomes]
rs4973576	0.88[EUR][1000 genomes]
rs709935	0.92[EUR][1000 genomes]
rs709936	0.92[EUR][1000 genomes]
rs778344	0.93[EUR][1000 genomes]
rs778345	0.93[EUR][1000 genomes]
rs778346	0.86[EUR][1000 genomes]
rs778347	0.92[EUR][1000 genomes]
rs778348	0.92[EUR][1000 genomes]
rs778350	0.92[EUR][1000 genomes]
rs778352	0.91[EUR][1000 genomes]
rs778355	0.90[EUR][1000 genomes]
rs778363	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs778364	0.82[AMR][1000 genomes];0.90[EUR][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	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3377192	chr2:233758324-233835472	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs778365	NGEF	cis	Adipose Subcutaneous	GTEx
rs778365	NGEF	cis	Esophagus Mucosa	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233757400-233776600	Weak transcription	Brain Angular Gyrus	brain
2	chr2:233759200-233784400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:233764000-233783800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:233766600-233776400	Weak transcription	Liver	Liver
5	chr2:233767000-233789000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:233767200-233776200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:233767200-233790400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:233769200-233775400	Weak transcription	Duodenum Mucosa	Duodenum

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