Variant report

Variant	rs4973569
Chromosome Location	chr2:233767037-233767038
allele	A/G
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	ETS1	chr2:233766676-233767081	A549	lung:	n/a	chr2:233766845-233766860
2	SP1	chr2:233766419-233767132	A549	lung:	n/a	n/a
3	POLR2A	chr2:233766262-233767328	U87	brain:	n/a	n/a
4	FOSL2	chr2:233766564-233767118	SK-N-SH	brain:	n/a	chr2:233766868-233766876 chr2:233766867-233766877 chr2:233766839-233766850 chr2:233766868-233766875
5	RFX5	chr2:233766719-233767088	Hela-S3	cervix:	n/a	chr2:233766890-233766907
6	JUND	chr2:233766663-233767072	A549	lung:	n/a	chr2:233766840-233766851 chr2:233766868-233766876 chr2:233766867-233766877 chr2:233766868-233766875
7	SP1	chr2:233766047-233767358	HCT-116	colon:	n/a	n/a
8	MYC	chr2:233766717-233767076	NB4	blood:	n/a	n/a
9	RXRA	chr2:233766187-233767230	SK-N-SH	brain:	n/a	n/a
10	JUND	chr2:233766585-233767105	A549	lung:	n/a	chr2:233766840-233766851 chr2:233766868-233766876 chr2:233766867-233766877 chr2:233766868-233766875
11	CHD2	chr2:233766474-233767106	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr2:233766324-233767089	HCT-116	colon:	n/a	n/a
13	RAD21	chr2:233766422-233767104	Hela-S3	cervix:	n/a	chr2:233766903-233766917 chr2:233766831-233766844 chr2:233767054-233767067
14	MAX	chr2:233766590-233767086	SK-N-SH	brain:	n/a	n/a
15	GABPA	chr2:233766628-233767090	A549	lung:	n/a	n/a
16	FOSL2	chr2:233766650-233767079	A549	lung:	n/a	chr2:233766868-233766876 chr2:233766867-233766877 chr2:233766839-233766850 chr2:233766868-233766875
17	POLR2A	chr2:233766475-233767118	HUVEC	blood vessel:	n/a	n/a
18	FOSL1	chr2:233766181-233767251	HCT-116	colon:	n/a	chr2:233766868-233766876 chr2:233766867-233766877 chr2:233766868-233766875
19	RCOR1	chr2:233766397-233767055	Hela-S3	cervix:	n/a	n/a
20	JUN	chr2:233766700-233767053	Hela-S3	cervix:	n/a	chr2:233766868-233766876 chr2:233766867-233766877 chr2:233766868-233766875
21	EP300	chr2:233766708-233767037	Hela-S3	cervix:	n/a	chr2:233766828-233766844
22	MAFK	chr2:233766678-233767041	Hela-S3	cervix:	n/a	chr2:233766869-233766878 chr2:233766868-233766878
23	MAX	chr2:233766730-233767107	NB4	blood:	n/a	n/a
24	POLR2A	chr2:233766269-233767121	HCT-116	colon:	n/a	n/a
25	TCF7L2	chr2:233766440-233767096	Hela-S3	cervix:	n/a	n/a
26	JUND	chr2:233766344-233767519	SK-N-SH	brain:	n/a	chr2:233766840-233766851 chr2:233766868-233766876 chr2:233766867-233766877 chr2:233766868-233766875
27	FOS	chr2:233766288-233767253	HUVEC	blood vessel:	n/a	chr2:233766868-233766876 chr2:233766867-233766877 chr2:233766866-233766877 chr2:233766868-233766875
28	FOSL2	chr2:233766391-233767311	A549	lung:	n/a	chr2:233766868-233766876 chr2:233766867-233766877 chr2:233766839-233766850 chr2:233766868-233766875
29	FOS	chr2:233766681-233767051	MCF10A-Er-Src	breast:	n/a	chr2:233766868-233766876 chr2:233766867-233766877 chr2:233766866-233766877 chr2:233766868-233766875
30	POLR2A	chr2:233766180-233767180	Hela-S3	cervix:	n/a	n/a
31	FOS	chr2:233766659-233767263	MCF10A-Er-Src	breast:	n/a	chr2:233766868-233766876 chr2:233766867-233766877 chr2:233766866-233766877 chr2:233766868-233766875
32	FOSL2	chr2:233766621-233767088	HepG2	liver:	n/a	chr2:233766868-233766876 chr2:233766867-233766877 chr2:233766839-233766850 chr2:233766868-233766875
33	CEBPB	chr2:233766717-233767061	A549	lung:	n/a	n/a
34	ELK1	chr2:233766776-233767120	Hela-S3	cervix:	n/a	n/a
35	FOSL1	chr2:233766268-233767381	HCT-116	colon:	n/a	chr2:233766868-233766876 chr2:233766867-233766877 chr2:233766868-233766875
36	POLR2A	chr2:233766201-233767258	IMR90	lung:	n/a	n/a
37	SMARCB1	chr2:233765736-233767195	Hela-S3	cervix:	n/a	n/a
38	JUND	chr2:233766012-233767321	HCT-116	colon:	n/a	chr2:233766840-233766851 chr2:233766868-233766876 chr2:233766867-233766877 chr2:233766868-233766875
39	JUN	chr2:233766717-233767049	K562	blood:	n/a	chr2:233766868-233766876 chr2:233766867-233766877 chr2:233766868-233766875
40	POLR2A	chr2:233766614-233767095	SK-N-SH	brain:	n/a	n/a
41	CEBPB	chr2:233766428-233767044	Hela-S3	cervix:	n/a	n/a
42	MAZ	chr2:233766033-233767102	IMR90	lung:	n/a	n/a
43	NR2F2	chr2:233766572-233767179	MCF-7	breast:	n/a	n/a
44	TCF7L2	chr2:233766151-233767259	HCT-116	colon:	n/a	n/a
45	EP300	chr2:233766650-233767063	SK-N-SH_RA	brain:	n/a	chr2:233766828-233766844
46	JUND	chr2:233766568-233767106	Hela-S3	cervix:	n/a	chr2:233766840-233766851 chr2:233766868-233766876 chr2:233766867-233766877 chr2:233766868-233766875
47	FOSL2	chr2:233766258-233767212	SK-N-SH	brain:	n/a	chr2:233766868-233766876 chr2:233766867-233766877 chr2:233766839-233766850 chr2:233766868-233766875
48	FOS	chr2:233766640-233767050	MCF10A-Er-Src	breast:	n/a	chr2:233766868-233766876 chr2:233766867-233766877 chr2:233766866-233766877 chr2:233766868-233766875
49	TFAP2C	chr2:233766231-233767055	Hela-S3	cervix:	n/a	chr2:233766832-233766847
50	POLR2A	chr2:233766262-233767360	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:233766884..233768683-chr2:233770434..233772099,2	K562	blood:

Variant related genes	Relation type
NGEF	TF binding region
ENSG00000066248	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1078323	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs1083522	0.91[CEU][hapmap]
rs11535	0.87[CEU][hapmap]
rs11689851	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13007579	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13024330	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1446309	1.00[CHB][hapmap]
rs17164	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2289911	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2344613	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2675954	0.91[CEU][hapmap];0.80[TSI][hapmap]
rs2675955	0.84[EUR][1000 genomes]
rs2675968	0.87[CEU][hapmap]
rs709937	0.87[CEU][hapmap]
rs748002	0.91[CEU][hapmap];0.80[TSI][hapmap]
rs778341	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs778370	0.87[CEU][hapmap]
rs778371	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs921055	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs938569	0.91[CEU][hapmap];0.80[TSI][hapmap]
rs938575	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv3437356	chr2:233762908-233767406	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4973569	TIGD1	cis	parietal	SCAN
rs4973569	CAB39	cis	cerebellum	SCAN
rs4973569	NGEF	cis	Esophagus Mucosa	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233757400-233776600	Weak transcription	Brain Angular Gyrus	brain
2	chr2:233758200-233768800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:233759200-233784400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:233764000-233768800	Weak transcription	Gastric	stomach
5	chr2:233764000-233783800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:233765400-233767200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:233765400-233767200	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr2:233765600-233767200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
9	chr2:233765600-233767200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:233765800-233767200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:233765800-233767400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:233765800-233767400	Enhancers	HMEC	breast
13	chr2:233765800-233767400	Enhancers	HUVEC	blood vessel
14	chr2:233765800-233767800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:233766000-233767200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:233766000-233767400	Enhancers	NHDF-Ad	bronchial
17	chr2:233766000-233767400	Enhancers	NHEK	skin
18	chr2:233766000-233767400	Enhancers	Osteobl	bone
19	chr2:233766000-233767600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:233766000-233767600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:233766200-233767200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
22	chr2:233766200-233767200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:233766200-233767200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:233766200-233767200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:233766200-233767200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:233766200-233767200	Enhancers	Brain Anterior Caudate	brain
27	chr2:233766200-233767200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:233766200-233767200	Enhancers	Spleen	Spleen
29	chr2:233766200-233767200	Flanking Active TSS	HSMM	muscle
30	chr2:233766200-233767400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:233766200-233767400	Flanking Active TSS	A549	lung
32	chr2:233766400-233767200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:233766400-233767200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
34	chr2:233766400-233767200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:233766400-233767200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr2:233766400-233767200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:233766400-233767200	Enhancers	Esophagus	oesophagus
38	chr2:233766400-233767200	Enhancers	HSMMtube	muscle
39	chr2:233766400-233767200	Flanking Active TSS	NH-A	brain
40	chr2:233766400-233767400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:233766600-233767200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
42	chr2:233766600-233767200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr2:233766600-233767200	Weak transcription	Colonic Mucosa	Colon
44	chr2:233766600-233767600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:233766600-233768600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr2:233766600-233776400	Weak transcription	Liver	Liver
47	chr2:233766800-233767200	Enhancers	HepG2	liver
48	chr2:233766800-233767200	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr2:233766800-233768000	Enhancers	Hela-S3	cervix
50	chr2:233767000-233767200	Flanking Active TSS	NHLF	lung

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