Variant report

Variant	rs2720022
Chromosome Location	chr12:122110011-122110012
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	BHLHE40	chr12:122109822-122110015	GM12878	blood:	n/a	n/a
2	GTF2F1	chr12:122109916-122110200	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr12:122109862-122110694	H1-hESC	embryonic stem cell:	n/a	chr12:122110552-122110561
4	KAP1	chr12:122109797-122110835	HEK293	kidney:	n/a	n/a
5	MXI1	chr12:122109738-122111743	SK-N-SH	brain:	n/a	n/a
6	FOS	chr12:122109748-122110048	MCF10A-Er-Src	breast:	n/a	n/a
7	YY1	chr12:122109939-122110715	H1-hESC	embryonic stem cell:	n/a	chr12:122110449-122110463
8	JUND	chr12:122109776-122110031	HepG2	liver:	n/a	n/a
9	E2F6	chr12:122109893-122110728	H1-hESC	embryonic stem cell:	n/a	n/a
10	FOS	chr12:122109701-122110073	MCF10A-Er-Src	breast:	n/a	n/a
11	SPI1	chr12:122109905-122110151	GM12878	blood:	n/a	chr12:122110032-122110041
12	SPI1	chr12:122109921-122110114	GM12891	blood:	n/a	chr12:122110032-122110041
13	ESRRA	chr12:122109520-122110261	GM12878	blood:	n/a	n/a
14	CREB1	chr12:122109641-122110220	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:122109997-122110133	GM12878	blood:	n/a	n/a
16	SIN3AK20	chr12:122109929-122110212	H1-hESC	embryonic stem cell:	n/a	n/a
17	GATA2	chr12:122110007-122110513	SH-SY5Y	brain:	n/a	chr12:122110029-122110039
18	STAT3	chr12:122109691-122110136	MCF10A-Er-Src	breast:	n/a	chr12:122110032-122110043
19	ELF1	chr12:122109956-122110838	GM12878	blood:	n/a	n/a
20	JUND	chr12:122109884-122110825	H1-hESC	embryonic stem cell:	n/a	n/a
21	SIN3A	chr12:122109838-122110693	H1-hESC	embryonic stem cell:	n/a	n/a
22	MTA3	chr12:122109780-122110867	GM12878	blood:	n/a	n/a
23	FOS	chr12:122109693-122110052	MCF10A-Er-Src	breast:	n/a	n/a
24	EP300	chr12:122109810-122110155	GM12878	blood:	n/a	chr12:122110027-122110041
25	SIN3A	chr12:122109924-122110094	GM12878	blood:	n/a	n/a
26	TBL1XR1	chr12:122109812-122110012	GM12878	blood:	n/a	n/a
27	EP300	chr12:122109807-122110014	GM12878	blood:	n/a	n/a
28	CHD2	chr12:122109901-122110101	GM12878	blood:	n/a	n/a
29	JUN	chr12:122109787-122110045	HepG2	liver:	n/a	chr12:122109902-122109915
30	POLR2A	chr12:122109819-122110122	H1-hESC	embryonic stem cell:	n/a	n/a
31	CEBPB	chr12:122109731-122110079	Hela-S3	cervix:	n/a	n/a
32	KAP1	chr12:122109830-122110741	U2OS	brain:	n/a	n/a
33	MXI1	chr12:122109903-122110139	GM12878	blood:	n/a	n/a
34	CEBPB	chr12:122109817-122110092	H1-hESC	embryonic stem cell:	n/a	n/a
35	GATA1	chr12:122109842-122110625	PBDE	blood:	n/a	chr12:122110029-122110039 chr12:122110596-122110606
36	STAT3	chr12:122109815-122110096	MCF10A-Er-Src	breast:	n/a	chr12:122110032-122110043
37	POLR2A	chr12:122109861-122110178	H1-hESC	embryonic stem cell:	n/a	n/a
38	TAF1	chr12:122109896-122110638	H1-hESC	embryonic stem cell:	n/a	n/a
39	CREB1	chr12:122109691-122110195	GM12878	blood:	n/a	n/a
40	EP300	chr12:122109734-122110040	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:122106004..122108217-chr12:122108294..122110534,2	MCF-7	breast:
2	chr12:122062970..122066467-chr12:122109966..122112755,3	MCF-7	breast:
3	chr12:121986936..121988892-chr12:122109089..122111571,2	MCF-7	breast:
4	chr12:121974913..121976672-chr12:122108817..122110319,2	MCF-7	breast:

Variant related genes	Relation type
MORN3	TF binding region
ENSG00000182500	Chromatin interaction
ENSG00000089094	Chromatin interaction
ENSG00000139714	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10743188	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10840652	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11043179	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12320939	0.94[ASW][hapmap];0.96[CEU][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs1877484	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2137434	0.80[MEX][hapmap]
rs2309142	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2466145	0.80[MEX][hapmap]
rs2669163	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2669165	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2669166	1.00[ASW][hapmap];0.89[CEU][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2669168	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2720021	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720025	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2720035	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2720041	0.88[MEX][hapmap];0.81[AMR][1000 genomes]
rs2942368	1.00[ASW][hapmap];0.96[CEU][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2942370	0.82[AMR][1000 genomes]
rs2942379	1.00[ASW][hapmap];0.89[CEU][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2954116	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3825175	0.94[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs3934658	0.88[ASW][hapmap];0.81[CEU][hapmap];0.96[MEX][hapmap]
rs6486789	0.84[EUR][1000 genomes]
rs7135617	0.81[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs7297028	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7397295	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7399127	0.88[ASW][hapmap];0.81[CEU][hapmap];0.96[MEX][hapmap]
rs7967415	0.80[MEX][hapmap]
rs7978609	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7978866	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs925531	0.84[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
3	nsv1040169	chr12:122096825-122209555	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2720022	GTF2H3	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122103200-122116000	Weak transcription	K562	blood
2	chr12:122109400-122110400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr12:122109400-122110400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
4	chr12:122109400-122111000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr12:122109400-122111200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
6	chr12:122109400-122111200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr12:122109600-122110200	Enhancers	Fetal Muscle Leg	muscle
8	chr12:122109600-122110200	Enhancers	Placenta Amnion	Placenta Amnion
9	chr12:122109600-122110400	Flanking Active TSS	NHEK	skin
10	chr12:122109800-122110200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:122109800-122110200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:122109800-122110200	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr12:122109800-122110200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr12:122109800-122110200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
15	chr12:122109800-122110200	Flanking Active TSS	Fetal Brain Female	brain
16	chr12:122109800-122110200	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr12:122109800-122110200	Enhancers	HSMM	muscle
18	chr12:122109800-122110200	Flanking Active TSS	NHDF-Ad	bronchial
19	chr12:122109800-122110400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr12:122109800-122110400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:122109800-122110400	Flanking Active TSS	Brain Anterior Caudate	brain
22	chr12:122109800-122110400	Flanking Active TSS	Brain Cingulate Gyrus	brain
23	chr12:122109800-122110400	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr12:122109800-122110400	Active TSS	Stomach Smooth Muscle	stomach
25	chr12:122109800-122110400	Flanking Active TSS	Osteobl	bone
26	chr12:122109800-122110800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:122109800-122110800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr12:122109800-122110800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:122109800-122111000	Active TSS	H9 Cell Line	embryonic stem cell
30	chr12:122109800-122111000	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr12:122109800-122111000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:122109800-122111000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:122109800-122111000	Active TSS	Brain Germinal Matrix	brain
34	chr12:122109800-122111000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:122109800-122111000	Active TSS	Fetal Kidney	kidney
36	chr12:122109800-122111000	Flanking Active TSS	Placenta	Placenta
37	chr12:122109800-122111000	Flanking Active TSS	GM12878-XiMat	blood
38	chr12:122109800-122111200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr12:122109800-122111200	Flanking Active TSS	Dnd41	blood
40	chr12:122109800-122111400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:122110000-122110200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr12:122110000-122110200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:122110000-122110200	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr12:122110000-122110200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr12:122110000-122110200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr12:122110000-122110200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:122110000-122110200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr12:122110000-122110200	Enhancers	Liver	Liver
49	chr12:122110000-122110200	Enhancers	Fetal Heart	heart
50	chr12:122110000-122110200	Enhancers	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links