Variant report

Variant	rs1878287
Chromosome Location	chr2:233790649-233790650
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:233790048..233791601-chr2:233794420..233796079,2	K562	blood:
2	chr2:233757939..233760469-chr2:233789148..233791862,2	K562	blood:
3	chr2:233725493..233728211-chr2:233788384..233791443,3	K562	blood:
4	chr2:233757939..233761647-chr2:233789148..233791862,3	K562	blood:

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

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

rs_ID	r²[population]
rs1980168	0.86[EUR][1000 genomes]
rs1980169	0.86[EUR][1000 genomes]
rs1996342	0.86[EUR][1000 genomes]
rs2102788	0.85[EUR][1000 genomes]
rs2592120	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2675959	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2675964	0.91[EUR][1000 genomes]
rs2675965	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2921705	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2944591	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4973576	0.86[EUR][1000 genomes]
rs709935	0.89[EUR][1000 genomes]
rs709936	0.89[EUR][1000 genomes]
rs778344	0.91[EUR][1000 genomes]
rs778345	0.90[EUR][1000 genomes]
rs778346	0.84[EUR][1000 genomes]
rs778347	0.89[EUR][1000 genomes]
rs778348	0.89[EUR][1000 genomes]
rs778350	0.89[EUR][1000 genomes]
rs778352	0.89[EUR][1000 genomes]
rs778355	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778363	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778364	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778365	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1878287	NGEF	cis	Esophagus Mucosa	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233781800-233791800	Weak transcription	Pancreas	Pancrea
2	chr2:233784000-233791400	Strong transcription	Liver	Liver
3	chr2:233785000-233792000	Weak transcription	Gastric	stomach
4	chr2:233789200-233791200	Bivalent Enhancer	Fetal Muscle Leg	muscle
5	chr2:233789200-233791400	Enhancers	Esophagus	oesophagus
6	chr2:233789200-233791600	Strong transcription	HepG2	liver
7	chr2:233789400-233791600	Enhancers	HSMMtube	muscle
8	chr2:233789800-233791400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
9	chr2:233789800-233791600	Active TSS	Brain Anterior Caudate	brain
10	chr2:233789800-233791600	Bivalent Enhancer	Fetal Intestine Small	intestine
11	chr2:233789800-233791800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
12	chr2:233789800-233791800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:233789800-233792000	Bivalent Enhancer	Fetal Intestine Large	intestine
14	chr2:233789800-233792400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr2:233789800-233793200	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr2:233790000-233790800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:233790000-233791600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:233790000-233791600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:233790000-233792000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
20	chr2:233790000-233792200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
21	chr2:233790200-233791400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
22	chr2:233790200-233791400	Active TSS	Brain Angular Gyrus	brain
23	chr2:233790200-233791600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
24	chr2:233790200-233791800	Bivalent Enhancer	Fetal Stomach	stomach
25	chr2:233790200-233791800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
26	chr2:233790200-233792000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:233790400-233791200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
28	chr2:233790400-233791400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:233790400-233792200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
30	chr2:233790400-233792400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
31	chr2:233790600-233790800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:233790600-233790800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:233790600-233790800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
34	chr2:233790600-233790800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
35	chr2:233790600-233791000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:233790600-233791000	Bivalent/Poised TSS	Fetal Brain Female	brain
37	chr2:233790600-233791400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
38	chr2:233790600-233791800	Bivalent Enhancer	Right Ventricle	heart
39	chr2:233790600-233792400	Bivalent Enhancer	Placenta	Placenta

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