Variant report

Variant	rs2592118
Chromosome Location	chr2:233792425-233792426
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1083514	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1083515	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1083517	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1083518	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1083519	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1083520	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1083521	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11675082	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1878289	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2004202	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2004203	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2592127	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2675960	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2880986	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2944590	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73102769	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs747462	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs747463	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs778353	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs895435	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
6	nsv1014548	chr2:233777859-233816018	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv518226	chr2:233790447-233793517	Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	esv3376153	chr2:233791333-233794081	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
9	esv3411164	chr2:233791958-233793981	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2592118	NGEF	cis	Esophagus Mucosa	GTEx
rs2592118	NGEF	cis	Artery Aorta	GTEx
rs2592118	NGEF	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233789800-233793200	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr2:233791000-233792600	Bivalent Enhancer	Fetal Brain Male	brain
3	chr2:233791200-233792800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
4	chr2:233791200-233793400	Bivalent/Poised TSS	NHLF	lung
5	chr2:233791200-233793800	Bivalent Enhancer	Spleen	Spleen
6	chr2:233791400-233792600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:233791400-233793000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
8	chr2:233791400-233793200	Weak transcription	Liver	Liver
9	chr2:233791400-233793600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:233791400-233793600	Bivalent Enhancer	Lung	lung
11	chr2:233791400-233794200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
12	chr2:233791600-233792600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:233791600-233792600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:233791600-233793200	Active TSS	A549	lung
15	chr2:233791600-233793600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr2:233791600-233798200	Weak transcription	HepG2	liver
17	chr2:233791800-233792600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:233791800-233792600	Bivalent Enhancer	Stomach Mucosa	stomach
19	chr2:233791800-233792800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:233791800-233793200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:233791800-233793200	Active TSS	Esophagus	oesophagus
22	chr2:233791800-233793400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
23	chr2:233791800-233793400	Bivalent/Poised TSS	Psoas Muscle	Psoas
24	chr2:233791800-233793600	Enhancers	Primary B cells from cord blood	blood
25	chr2:233791800-233793600	Enhancers	Fetal Heart	heart
26	chr2:233791800-233793800	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:233791800-233794000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
28	chr2:233791800-233794000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
29	chr2:233791800-233794000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:233792000-233792600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:233792000-233792600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:233792000-233792600	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:233792000-233792600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
34	chr2:233792000-233792600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
35	chr2:233792000-233792600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
36	chr2:233792000-233792800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:233792000-233792800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:233792000-233792800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:233792000-233792800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:233792000-233793000	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:233792000-233793000	Bivalent/Poised TSS	Right Ventricle	heart
42	chr2:233792000-233793200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:233792000-233793200	Active TSS	Brain Cingulate Gyrus	brain
44	chr2:233792000-233793200	Bivalent/Poised TSS	Placenta Amnion	Placenta Amnion
45	chr2:233792000-233793200	Active TSS	HSMM	muscle
46	chr2:233792000-233793400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:233792000-233793400	Active TSS	Brain Substantia Nigra	brain
48	chr2:233792000-233793600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
49	chr2:233792000-233793600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:233792000-233793600	Active TSS	Brain Anterior Caudate	brain

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