Variant report

Variant	rs2675965
Chromosome Location	chr2:233793736-233793737
allele	C/T
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	MAX	chr2:233793559-233794276	H1-hESC	embryonic stem cell:	n/a	chr2:233794117-233794126 chr2:233794116-233794125 chr2:233794114-233794129 chr2:233794116-233794126 chr2:233794112-233794127 chr2:233794115-233794125
2	MAX	chr2:233793359-233794290	H1-hESC	embryonic stem cell:	n/a	chr2:233794117-233794126 chr2:233794116-233794125 chr2:233794114-233794129 chr2:233794116-233794126 chr2:233794112-233794127 chr2:233794115-233794125

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:233792964..233795634-chr2:233797623..233799367,2	K562	blood:

Variant related genes	Relation type
NGEF	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1878287	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1980168	0.93[EUR][1000 genomes]
rs1980169	0.93[EUR][1000 genomes]
rs1996342	0.93[EUR][1000 genomes]
rs2102788	0.92[EUR][1000 genomes]
rs2592120	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2675959	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2675964	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2921705	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2944591	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4973576	0.93[EUR][1000 genomes]
rs709935	0.96[EUR][1000 genomes]
rs709936	0.96[EUR][1000 genomes]
rs778344	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs778345	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs778346	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs778347	0.96[EUR][1000 genomes]
rs778348	0.96[EUR][1000 genomes]
rs778350	0.96[EUR][1000 genomes]
rs778352	0.96[EUR][1000 genomes]
rs778355	0.91[EUR][1000 genomes]
rs778363	0.91[EUR][1000 genomes]
rs778364	0.91[EUR][1000 genomes]
rs778365	0.93[EUR][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	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
8	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2675965	NGEF	cis	Esophagus Mucosa	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233791200-233793800	Bivalent Enhancer	Spleen	Spleen
2	chr2:233791400-233794200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
3	chr2:233791600-233798200	Weak transcription	HepG2	liver
4	chr2:233791800-233793800	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:233791800-233794000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr2:233791800-233794000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr2:233791800-233794000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:233792000-233793800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr2:233792000-233794000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
10	chr2:233792400-233794400	Enhancers	Pancreas	Pancrea
11	chr2:233792400-233796000	Weak transcription	HSMMtube	muscle
12	chr2:233792400-233798000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr2:233793000-233793800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:233793000-233793800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
15	chr2:233793000-233794200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
16	chr2:233793200-233793800	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:233793200-233793800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:233793200-233793800	Enhancers	Esophagus	oesophagus
19	chr2:233793200-233793800	Bivalent Enhancer	Placenta	Placenta
20	chr2:233793200-233794200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr2:233793400-233793800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
22	chr2:233793400-233793800	Bivalent/Poised TSS	Right Ventricle	heart
23	chr2:233793400-233793800	Bivalent Enhancer	Thymus	Thymus
24	chr2:233793400-233794200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
25	chr2:233793400-233794200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:233793400-233794400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:233793400-233794400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
28	chr2:233793400-233795800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:233793400-233796000	Weak transcription	Right Atrium	heart
30	chr2:233793600-233793800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:233793600-233793800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
32	chr2:233793600-233793800	Bivalent Enhancer	Primary B cells from cord blood	blood
33	chr2:233793600-233793800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:233793600-233793800	Bivalent Enhancer	Fetal Intestine Small	intestine
35	chr2:233793600-233793800	Bivalent Enhancer	Fetal Muscle Leg	muscle
36	chr2:233793600-233794000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
37	chr2:233793600-233794200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
38	chr2:233793600-233794400	Bivalent Enhancer	Fetal Brain Female	brain
39	chr2:233793600-233794400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
40	chr2:233793600-233805600	Weak transcription	Liver	Liver
41	chr2:233793600-233806400	Weak transcription	Gastric	stomach

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