Variant report

Variant	rs3792095
Chromosome Location	chr2:234238949-234238950
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	TCF12	chr2:234238159-234238956	ECC-1	luminal epithelium:	n/a	chr2:234238581-234238588
2	POLR2A	chr2:234238861-234239350	SK-N-MC	brain:	n/a	n/a
3	PRDM1	chr2:234238926-234239116	Hela-S3	cervix:	n/a	chr2:234239048-234239057 chr2:234239049-234239058
4	CTBP2	chr2:234238246-234239056	H1-hESC	embryonic stem cell:	n/a	n/a
5	JUND	chr2:234238918-234239110	HepG2	liver:	n/a	chr2:234239047-234239059 chr2:234239042-234239054 chr2:234239049-234239058 chr2:234239050-234239057 chr2:234239047-234239058 chr2:234239048-234239057 chr2:234239048-234239058 chr2:234239045-234239056
6	TEAD4	chr2:234238149-234239202	ECC-1	luminal epithelium:	n/a	n/a
7	TCF12	chr2:234238078-234239071	ECC-1	luminal epithelium:	n/a	chr2:234238581-234238588
8	JUND	chr2:234238895-234239215	Hela-S3	cervix:	n/a	chr2:234239047-234239059 chr2:234239042-234239054 chr2:234239049-234239058 chr2:234239050-234239057 chr2:234239047-234239058 chr2:234239048-234239057 chr2:234239048-234239058 chr2:234239045-234239056
9	MAX	chr2:234238299-234239237	ECC-1	luminal epithelium:	n/a	n/a
10	EP300	chr2:234238073-234239096	ECC-1	luminal epithelium:	n/a	chr2:234238267-234238281 chr2:234239048-234239057
11	NFIC	chr2:234238137-234238987	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:234238246..234240780-chr2:234263095..234264681,2	K562	blood:
2	chr2:234209576..234212564-chr2:234237690..234239510,2	MCF-7	breast:
3	chr2:234237506..234239939-chr2:234241158..234243320,2	K562	blood:

Variant related genes	Relation type
SAG	TF binding region
ENSG00000077044	Chromatin interaction
ENSG00000243637	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10168794	0.84[ASN][1000 genomes]
rs10185174	0.84[ASN][1000 genomes]
rs13384932	0.84[ASN][1000 genomes]
rs13420976	0.84[ASN][1000 genomes]
rs13427703	1.00[ASN][1000 genomes]
rs2289473	0.92[ASN][1000 genomes]
rs28437319	0.84[ASN][1000 genomes]
rs28605452	1.00[ASN][1000 genomes]
rs28657808	0.84[ASN][1000 genomes]
rs3762586	1.00[ASN][1000 genomes]
rs3792104	0.92[ASN][1000 genomes]
rs56871749	0.84[ASN][1000 genomes]
rs57712949	0.84[ASN][1000 genomes]
rs58222850	0.84[ASN][1000 genomes]
rs6431282	0.92[ASN][1000 genomes]
rs6745134	0.84[ASN][1000 genomes]
rs73106630	0.84[ASN][1000 genomes]
rs73110043	0.81[EUR][1000 genomes]
rs73998327	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584699	chr2:234182240-234255547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002075	chr2:234225979-234277508	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3792095	NGEF	cis	intralobular white matter	BrainEAC

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234223600-234245400	Weak transcription	Pancreas	Pancrea
2	chr2:234228400-234240000	Weak transcription	Fetal Intestine Small	intestine
3	chr2:234234400-234239800	Weak transcription	Thymus	Thymus
4	chr2:234237200-234242800	Enhancers	Spleen	Spleen
5	chr2:234237400-234249800	Enhancers	Primary B cells from peripheral blood	blood
6	chr2:234237600-234239000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
7	chr2:234237600-234239200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
8	chr2:234237600-234239600	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr2:234237800-234239000	Enhancers	H9 Cell Line	embryonic stem cell
10	chr2:234237800-234239600	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr2:234237800-234240000	Enhancers	Primary T cells fromperipheralblood	blood
12	chr2:234237800-234244000	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr2:234238000-234239000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:234238000-234239000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:234238000-234239000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
16	chr2:234238000-234239000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:234238000-234239000	Enhancers	HSMM	muscle
18	chr2:234238000-234240000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:234238200-234239000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:234238200-234239000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr2:234238200-234239000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:234238200-234239000	Enhancers	NH-A	brain
23	chr2:234238200-234240000	Enhancers	Primary B cells from cord blood	blood
24	chr2:234238200-234240000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:234238200-234240000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr2:234238200-234240200	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr2:234238400-234239800	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr2:234238400-234239800	Weak transcription	Fetal Thymus	thymus
29	chr2:234238400-234240000	Enhancers	Primary T cells from cord blood	blood
30	chr2:234238400-234243000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:234238400-234244600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:234238600-234239000	Enhancers	Hela-S3	cervix
33	chr2:234238600-234239600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr2:234238600-234239800	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr2:234238600-234239800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:234238600-234239800	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr2:234238600-234240000	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr2:234238600-234240000	Weak transcription	Placenta	Placenta
39	chr2:234238600-234241000	Weak transcription	Fetal Muscle Leg	muscle
40	chr2:234238800-234239000	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr2:234238800-234239000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
42	chr2:234238800-234239000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
43	chr2:234238800-234239200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
44	chr2:234238800-234240000	Weak transcription	K562	blood
45	chr2:234238800-234243600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr2:234238800-234246600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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