Variant report

Variant	rs2675955
Chromosome Location	chr2:233753281-233753282
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	chr2:233751474-233753914	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:233753215-233753304	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr2:233752633-233753414	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:233746909..233748527-chr2:233752427..233754026,2	MCF-7	breast:
2	chr2:233746656..233750390-chr2:233751961..233755416,5	K562	blood:
3	chr2:233748622..233750691-chr2:233751961..233754104,3	K562	blood:

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

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2675954	0.82[EUR][1000 genomes]
rs4973569	0.84[EUR][1000 genomes]
rs748002	0.82[EUR][1000 genomes]
rs778341	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs778371	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs938569	0.82[EUR][1000 genomes]
rs938575	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1009825	chr2:233709566-233763470	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv984452	chr2:233725452-233762965	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv999116	chr2:233733352-233759864	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1007029	chr2:233733352-233760519	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv536179	chr2:233735380-233757170	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv3375822	chr2:233750908-233755306	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2675955	NGEF	cis	Esophagus Mucosa	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233726800-233755600	Weak transcription	HSMMtube	muscle
2	chr2:233742400-233754200	Strong transcription	Fetal Intestine Small	intestine
3	chr2:233742400-233755600	Weak transcription	Fetal Intestine Large	intestine
4	chr2:233742600-233753400	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr2:233742800-233755600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr2:233743000-233755800	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:233743200-233759600	Strong transcription	Duodenum Mucosa	Duodenum
8	chr2:233744600-233755400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:233745200-233755600	Weak transcription	Brain Angular Gyrus	brain
10	chr2:233745200-233755800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:233745600-233759800	Strong transcription	Liver	Liver
12	chr2:233749200-233755600	Weak transcription	NHLF	lung
13	chr2:233749400-233766000	Weak transcription	A549	lung
14	chr2:233749800-233753400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:233750000-233755600	Weak transcription	Brain Germinal Matrix	brain
16	chr2:233750600-233755400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:233750600-233759800	Strong transcription	HepG2	liver
18	chr2:233750800-233761000	Weak transcription	Stomach Mucosa	stomach
19	chr2:233751000-233755600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:233751000-233766000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr2:233751200-233753400	Strong transcription	Esophagus	oesophagus
22	chr2:233751200-233755400	Weak transcription	Pancreas	Pancrea
23	chr2:233751200-233755600	Weak transcription	Fetal Brain Female	brain
24	chr2:233751200-233755600	Weak transcription	Gastric	stomach
25	chr2:233751200-233758400	Weak transcription	Fetal Brain Male	brain
26	chr2:233751800-233755800	Weak transcription	Right Atrium	heart
27	chr2:233752400-233754400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:233752800-233753400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:233752800-233753400	Enhancers	Spleen	Spleen
30	chr2:233753000-233753400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:233753000-233753400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:233753200-233753400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:233753200-233753400	Active TSS	Brain Anterior Caudate	brain
34	chr2:233753200-233754800	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr2:233753200-233755400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr2:233753200-233755400	Weak transcription	Colonic Mucosa	Colon
37	chr2:233753200-233755600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr2:233753200-233757200	Weak transcription	Rectal Mucosa Donor 31	rectum

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