Variant report

Variant	rs2592127
Chromosome Location	chr2:233791648-233791649
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:233757939..233760469-chr2:233789148..233791862,2	K562	blood:
2	chr2:233757939..233761647-chr2:233789148..233791862,3	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1083514	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1083515	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1083517	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1083518	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1083519	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1083520	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1083521	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11675082	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1878289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2004202	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2004203	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2592118	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2675960	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2880986	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2944590	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73102769	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs747462	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747463	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778353	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs895435	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2592127	NGEF	cis	Esophagus Mucosa	GTEx
rs2592127	NGEF	cis	Adipose Subcutaneous	GTEx
rs2592127	NGEF	cis	Artery Aorta	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233781800-233791800	Weak transcription	Pancreas	Pancrea
2	chr2:233785000-233792000	Weak transcription	Gastric	stomach
3	chr2:233789800-233791800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
4	chr2:233789800-233791800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:233789800-233792000	Bivalent Enhancer	Fetal Intestine Large	intestine
6	chr2:233789800-233792400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr2:233789800-233793200	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr2:233790000-233792000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
9	chr2:233790000-233792200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
10	chr2:233790200-233791800	Bivalent Enhancer	Fetal Stomach	stomach
11	chr2:233790200-233791800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
12	chr2:233790200-233792000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:233790400-233792200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
14	chr2:233790400-233792400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
15	chr2:233790600-233791800	Bivalent Enhancer	Right Ventricle	heart
16	chr2:233790600-233792400	Bivalent Enhancer	Placenta	Placenta
17	chr2:233791000-233791800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:233791000-233792400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
19	chr2:233791000-233792400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
20	chr2:233791000-233792600	Bivalent Enhancer	Fetal Brain Male	brain
21	chr2:233791200-233791800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
22	chr2:233791200-233791800	Bivalent Enhancer	Primary B cells from cord blood	blood
23	chr2:233791200-233791800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
24	chr2:233791200-233792000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
25	chr2:233791200-233792000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
26	chr2:233791200-233792000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:233791200-233792000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:233791200-233792200	Bivalent Enhancer	Small Intestine	intestine
29	chr2:233791200-233792400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
30	chr2:233791200-233792400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
31	chr2:233791200-233792800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
32	chr2:233791200-233793400	Bivalent/Poised TSS	NHLF	lung
33	chr2:233791200-233793800	Bivalent Enhancer	Spleen	Spleen
34	chr2:233791400-233791800	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
35	chr2:233791400-233791800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
36	chr2:233791400-233791800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
37	chr2:233791400-233791800	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:233791400-233791800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
39	chr2:233791400-233791800	Flanking Active TSS	Esophagus	oesophagus
40	chr2:233791400-233792000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:233791400-233792000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
42	chr2:233791400-233792000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:233791400-233792000	Flanking Bivalent TSS/Enh	Brain Substantia Nigra	brain
44	chr2:233791400-233792000	Flanking Active TSS	HSMM	muscle
45	chr2:233791400-233792200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:233791400-233792200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
47	chr2:233791400-233792200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:233791400-233792200	Bivalent Enhancer	Adipose Nuclei	Adipose
49	chr2:233791400-233792200	Flanking Active TSS	Brain Angular Gyrus	brain
50	chr2:233791400-233792600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell

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