Variant report

Variant	rs11057222
Chromosome Location	chr12:123752905-123752906
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	chr12:123752639-123752917	H1-hESC	embryonic stem cell:	n/a	n/a
2	SPI1	chr12:123752698-123753116	HL-60	blood:	n/a	chr12:123752867-123752880
3	POLR2A	chr12:123752685-123753001	HUVEC	blood vessel:	n/a	n/a
4	RUNX3	chr12:123752557-123752976	GM12878	blood:	n/a	n/a
5	MXI1	chr12:123751836-123757238	SK-N-SH	brain:	n/a	chr12:123755352-123755361
6	POLR2A	chr12:123752530-123752955	HUVEC	blood vessel:	n/a	n/a
7	REST	chr12:123752406-123752937	SK-N-SH	brain:	n/a	chr12:123752700-123752709
8	TCF3	chr12:123752597-123752981	GM12878	blood:	n/a	n/a
9	RUNX3	chr12:123752534-123752951	GM12878	blood:	n/a	n/a
10	TCF3	chr12:123752672-123752907	GM12878	blood:	n/a	n/a
11	EBF1	chr12:123752603-123753025	GM12878	blood:	n/a	n/a
12	MYC	chr12:123752717-123752917	NB4	blood:	n/a	n/a
13	POLR2A	chr12:123752762-123757235	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr12:123752165-123757291	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr12:123752659-123752909	GM12878	blood:	n/a	n/a
16	MTA3	chr12:123752878-123754285	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:123752887..123754431-chr12:123868251..123870818,2	K562	blood:
2	chr12:123717082..123719698-chr12:123751267..123753093,2	K562	blood:
3	chr12:123736848..123739836-chr12:123749677..123753155,4	K562	blood:
4	chr12:123749757..123758492-chr12:123844437..123851411,15	MCF-7	breast:

Variant related genes	Relation type
CDK2AP1	TF binding region
ENSG00000130921	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000256092	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10083067	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846476	0.81[ASN][1000 genomes]
rs10846477	0.81[ASN][1000 genomes]
rs10846479	0.81[ASN][1000 genomes]
rs10846490	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846492	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846493	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10846494	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11057214	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11531106	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61953388	0.87[AMR][1000 genomes];0.91[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	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	esv1836043	chr12:123709409-123822503	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11057222	CDK2AP1	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123734600-123753200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:123737000-123753000	Strong transcription	Fetal Intestine Small	intestine
3	chr12:123739200-123753000	Weak transcription	Right Atrium	heart
4	chr12:123739200-123753200	Weak transcription	Fetal Heart	heart
5	chr12:123739200-123754200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:123739800-123753200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr12:123740000-123753600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:123741000-123753600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr12:123742400-123753400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr12:123742400-123754600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:123742400-123754600	Weak transcription	Small Intestine	intestine
12	chr12:123743000-123754200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr12:123743400-123754000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr12:123743600-123753600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr12:123744000-123753800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr12:123744000-123753800	Weak transcription	K562	blood
17	chr12:123745000-123753000	Weak transcription	Stomach Mucosa	stomach
18	chr12:123745400-123754000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:123746200-123753200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:123746600-123753000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:123746600-123754000	Weak transcription	Fetal Kidney	kidney
22	chr12:123746800-123753000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
23	chr12:123747000-123753400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr12:123747000-123754400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr12:123748400-123753000	Weak transcription	Colon Smooth Muscle	Colon
26	chr12:123748400-123753200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:123748400-123753400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:123749200-123753800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:123749400-123754600	Enhancers	Fetal Brain Male	brain
30	chr12:123749800-123753000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr12:123750400-123753800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:123750600-123753200	Genic enhancers	Esophagus	oesophagus
33	chr12:123750600-123753400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:123750600-123753800	Weak transcription	Hela-S3	cervix
35	chr12:123750800-123753000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:123750800-123753400	Genic enhancers	Gastric	stomach
37	chr12:123751000-123753800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr12:123751400-123753000	Weak transcription	Ovary	ovary
39	chr12:123751400-123753800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:123751400-123753800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:123751400-123753800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:123751800-123753000	Weak transcription	Colonic Mucosa	Colon
43	chr12:123751800-123753200	Weak transcription	Liver	Liver
44	chr12:123751800-123753400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:123751800-123753600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr12:123751800-123753600	Weak transcription	Fetal Intestine Large	intestine
47	chr12:123751800-123753600	Genic enhancers	Fetal Stomach	stomach
48	chr12:123751800-123754200	Weak transcription	Aorta	Aorta
49	chr12:123751800-123754200	Flanking Active TSS	HSMMtube	muscle
50	chr12:123752000-123753000	Weak transcription	H1 Cell Line	embryonic stem cell

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