Variant report

Variant	rs2012423
Chromosome Location	chr2:233566914-233566915
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	POLR2A	chr2:233566623-233567013	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:233564546..233567333-chr2:233571993..233574146,2	K562	blood:
2	chr2:233565184..233567187-chr2:233578536..233582412,3	MCF-7	breast:
3	chr2:233561154..233564737-chr2:233566503..233568685,5	K562	blood:
4	chr2:233562305..233563943-chr2:233565378..233568018,2	MCF-7	breast:

Variant related genes	Relation type
GIGYF2	TF binding region
ENSG00000204120	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1022329	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10427328	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10933406	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1104764	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12105766	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62193269	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6704763	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6710294	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6717048	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6733495	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6739794	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]

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	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

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233563200-233567600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr2:233563200-233569000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:233563200-233572400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:233563400-233568600	Weak transcription	Aorta	Aorta
5	chr2:233563400-233569000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:233563800-233567600	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr2:233563800-233567600	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr2:233563800-233582600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:233564000-233568200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr2:233564000-233568600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr2:233564000-233568800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:233564000-233570600	Weak transcription	Fetal Kidney	kidney
13	chr2:233564000-233570800	Weak transcription	HSMMtube	muscle
14	chr2:233564000-233579600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:233564000-233589000	Weak transcription	NH-A	brain
16	chr2:233564200-233567200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:233564200-233567200	Weak transcription	Fetal Thymus	thymus
18	chr2:233564200-233567600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:233564200-233567800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr2:233564200-233567800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr2:233564200-233568200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr2:233564200-233568400	Weak transcription	Colonic Mucosa	Colon
23	chr2:233564200-233568400	Weak transcription	Fetal Muscle Leg	muscle
24	chr2:233564200-233568600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:233564200-233568600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:233564200-233568600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:233564200-233568600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:233564200-233568600	Weak transcription	Esophagus	oesophagus
29	chr2:233564200-233568600	Weak transcription	Lung	lung
30	chr2:233564200-233568800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:233564200-233570000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr2:233564200-233570400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr2:233564200-233571000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:233564200-233596400	Weak transcription	NHLF	lung
35	chr2:233564200-233613000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr2:233564400-233567000	Weak transcription	Primary B cells from cord blood	blood
37	chr2:233564400-233568000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr2:233564600-233567400	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr2:233564800-233568800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:233564800-233569400	Weak transcription	Osteobl	bone
41	chr2:233564800-233592800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr2:233565000-233567600	Weak transcription	Right Atrium	heart
43	chr2:233565000-233568200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:233565000-233568400	Weak transcription	Gastric	stomach
45	chr2:233565000-233568400	Weak transcription	NHDF-Ad	bronchial
46	chr2:233565000-233568800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:233565000-233612200	Weak transcription	Fetal Brain Male	brain
48	chr2:233565200-233567200	Weak transcription	HSMM	muscle
49	chr2:233565200-233567600	Weak transcription	GM12878-XiMat	blood
50	chr2:233565200-233568000	Weak transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links