Variant report

Variant	rs13026313
Chromosome Location	chr2:40009041-40009042
allele	A/C
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	CEBPB	chr2:40008783-40009170	A549	lung:	n/a	chr2:40008985-40008998 chr2:40008986-40008997 chr2:40008985-40008996
2	CEBPB	chr2:40008797-40009157	K562	blood:	n/a	chr2:40008985-40008998 chr2:40008986-40008997 chr2:40008985-40008996
3	KAP1	chr2:40008975-40009481	U2OS	brain:	n/a	n/a
4	CEBPB	chr2:40008756-40009176	HepG2	liver:	n/a	chr2:40008985-40008998 chr2:40008986-40008997 chr2:40008985-40008996
5	CEBPB	chr2:40008839-40009169	IMR90	lung:	n/a	chr2:40008985-40008998 chr2:40008986-40008997 chr2:40008985-40008996
6	STAT3	chr2:40008889-40009065	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr2:40008968-40009168	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr2:40008887-40009067	MCF10A-Er-Src	breast:	n/a	n/a
9	CEBPB	chr2:40008802-40009186	K562	blood:	n/a	chr2:40008985-40008998 chr2:40008986-40008997 chr2:40008985-40008996

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:40004284..40008257-chr2:40008263..40012278,6	MCF-7	breast:

Variant related genes	Relation type
THUMPD2	TF binding region
SLC8A1-AS1	TF binding region
ENSG00000138050	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10164984	0.81[EUR][1000 genomes]
rs10169390	0.85[EUR][1000 genomes]
rs10174709	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10207589	0.92[CEU][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10211306	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1035138	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1035139	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11124693	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11684302	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs12470473	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12620957	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12623462	0.82[ASN][1000 genomes]
rs12623545	0.82[ASN][1000 genomes]
rs12624217	0.88[CEU][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12712653	0.81[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs12712656	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs13425906	0.81[ASN][1000 genomes]
rs13428837	0.81[EUR][1000 genomes]
rs1548877	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17478972	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs1861243	0.81[EUR][1000 genomes]
rs1861258	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs1986876	0.84[CEU][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs2041735	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2058620	0.84[CEU][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs2110656	0.81[CEU][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2192685	0.84[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs2241115	0.83[JPT][hapmap]
rs2373689	0.92[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2540226	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2540227	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2540228	0.85[EUR][1000 genomes]
rs2716729	0.85[EUR][1000 genomes]
rs2716730	0.88[CEU][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs35761077	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3732121	0.88[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3732122	0.92[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4670955	0.81[ASN][1000 genomes]
rs4670956	0.84[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4670957	0.83[JPT][hapmap]
rs4670958	0.90[CHD][hapmap];0.83[JPT][hapmap]
rs4670959	0.88[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59756273	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6544242	0.92[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6719179	0.84[CEU][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs6722610	0.85[CEU][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes]
rs6731026	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6731450	0.83[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6747842	0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6750252	0.85[ASN][1000 genomes]
rs6758453	0.81[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs727376	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7560642	0.96[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7565954	0.87[CHD][hapmap];0.83[JPT][hapmap]
rs7581406	0.80[ASN][1000 genomes]
rs7590912	0.84[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs7591296	0.84[EUR][1000 genomes]
rs7591347	0.86[EUR][1000 genomes]
rs8265	0.89[CEU][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs917960	0.84[CEU][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs917962	0.84[CEU][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs917963	0.83[JPT][hapmap]
rs9309042	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs962262	0.81[CEU][hapmap];0.89[JPT][hapmap]
rs997976	0.92[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.90[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	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv873890	chr2:39976810-40009041	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv2696	chr2:39988381-40033288	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13026313	EIF2AK2	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40006600-40010000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:40006800-40010200	Weak transcription	Esophagus	oesophagus
3	chr2:40006800-40014000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:40007000-40010000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:40007000-40010000	Weak transcription	NHEK	skin
6	chr2:40007000-40010200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:40007000-40010200	Weak transcription	Placenta	Placenta
8	chr2:40007000-40010400	Weak transcription	NH-A	brain
9	chr2:40007200-40009400	Weak transcription	Brain Angular Gyrus	brain
10	chr2:40007200-40010000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:40007800-40010600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:40008000-40009200	Enhancers	Fetal Muscle Leg	muscle
13	chr2:40008000-40010000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr2:40008000-40010600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:40008200-40010400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:40008400-40010000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:40008400-40010600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:40008600-40009200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr2:40008600-40009200	Enhancers	Fetal Thymus	thymus
20	chr2:40008600-40009200	Enhancers	Thymus	Thymus
21	chr2:40008600-40009200	Flanking Active TSS	HepG2	liver
22	chr2:40008600-40010000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:40008600-40010000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr2:40008600-40010000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:40008600-40010000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr2:40008600-40010000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr2:40008600-40010200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr2:40008600-40010200	Weak transcription	HSMMtube	muscle
29	chr2:40008600-40010400	Weak transcription	NHDF-Ad	bronchial
30	chr2:40008800-40009200	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr2:40008800-40009200	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr2:40008800-40009200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:40008800-40009200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:40008800-40009200	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr2:40008800-40009200	Enhancers	Fetal Kidney	kidney
36	chr2:40008800-40009800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:40008800-40010000	Weak transcription	HMEC	breast
38	chr2:40008800-40010200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:40008800-40010200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr2:40008800-40010600	Enhancers	K562	blood
41	chr2:40008800-40013200	Weak transcription	Primary hematopoietic stem cells	blood
42	chr2:40009000-40009200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr2:40009000-40009200	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr2:40009000-40010600	Enhancers	Osteobl	bone
45	chr2:40009000-40013200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links