Variant report

Variant	rs12470473
Chromosome Location	chr2:40005290-40005291
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39956738..39958463-chr2:40003948..40005760,2	K562	blood:
2	chr2:39961424..39963272-chr2:40004019..40005990,2	K562	blood:
3	chr2:39739040..39741917-chr2:40004865..40006467,2	K562	blood:

Variant related genes	Relation type
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10164984	0.84[EUR][1000 genomes]
rs10169390	0.87[EUR][1000 genomes]
rs10174709	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10206408	0.80[ASN][1000 genomes]
rs10207589	0.92[CEU][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs10211306	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1035138	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1035139	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11124691	0.81[ASN][1000 genomes]
rs11124692	0.80[EUR][1000 genomes]
rs11124693	0.96[CEU][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11684302	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12620957	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12623462	0.84[ASN][1000 genomes]
rs12623545	0.84[ASN][1000 genomes]
rs12624217	0.88[CEU][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12712653	0.81[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs12712656	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs13026313	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]
rs13425906	0.81[ASN][1000 genomes]
rs13428837	0.84[EUR][1000 genomes]
rs1548877	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17478972	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs1861243	0.84[EUR][1000 genomes]
rs1861258	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs1986876	0.84[CEU][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2041735	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2058620	0.84[CEU][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2110656	0.81[CEU][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2192685	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs2241115	0.83[JPT][hapmap]
rs2373689	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2540226	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2540227	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2540228	0.87[EUR][1000 genomes]
rs2716729	0.87[EUR][1000 genomes]
rs2716730	0.88[CEU][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs35761077	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3732121	0.88[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3732122	0.92[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4670955	0.81[ASN][1000 genomes]
rs4670956	0.84[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4670957	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs4670958	0.93[CHD][hapmap];0.83[JPT][hapmap]
rs4670959	0.88[CEU][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59756273	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6544242	0.92[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6719179	0.84[CEU][hapmap];0.96[CHD][hapmap];0.83[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6722610	0.84[CEU][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes]
rs6731026	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6731450	0.83[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6747842	0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6750252	0.85[ASN][1000 genomes]
rs6758453	0.81[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs727376	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7560642	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7565954	0.90[CHD][hapmap];0.83[JPT][hapmap]
rs7581406	0.82[ASN][1000 genomes]
rs7590912	0.84[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs7591296	0.84[EUR][1000 genomes]
rs7591347	0.89[EUR][1000 genomes]
rs8265	0.89[CEU][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs917960	0.84[CEU][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs917962	0.84[CEU][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.85[EUR][1000 genomes]
rs917963	0.83[JPT][hapmap]
rs9309042	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs962262	0.81[CEU][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs997976	0.92[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12470473	EIF2AK2	cis	parietal	SCAN
rs12470473	THUMPD2	cis	brain	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39965200-40005400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:39985800-40005400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:39985800-40005400	Weak transcription	Lung	lung
4	chr2:39997000-40005400	Weak transcription	Placenta	Placenta
5	chr2:39997000-40005800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:39999000-40005400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:40000000-40006000	Weak transcription	Spleen	Spleen
8	chr2:40000200-40006000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:40001000-40006600	Active TSS	GM12878-XiMat	blood
10	chr2:40001400-40005400	Weak transcription	Gastric	stomach
11	chr2:40001400-40005400	Weak transcription	Left Ventricle	heart
12	chr2:40002800-40005400	Weak transcription	Esophagus	oesophagus
13	chr2:40002800-40005400	Weak transcription	Pancreas	Pancrea
14	chr2:40003600-40005400	Flanking Active TSS	Dnd41	blood
15	chr2:40003800-40005800	Enhancers	Small Intestine	intestine
16	chr2:40004000-40006000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:40004200-40005400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:40004200-40005400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr2:40004200-40006600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:40004200-40006600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:40004200-40006600	Active TSS	HSMMtube	muscle
22	chr2:40004200-40008800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:40004400-40005400	Enhancers	Primary B cells from peripheral blood	blood
24	chr2:40004400-40005400	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr2:40004400-40005600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr2:40004400-40005600	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr2:40004400-40005600	Flanking Active TSS	NH-A	brain
28	chr2:40004400-40005600	Flanking Active TSS	Osteobl	bone
29	chr2:40004400-40005800	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr2:40004400-40005800	Flanking Active TSS	HUVEC	blood vessel
31	chr2:40004400-40006600	Active TSS	HMEC	breast
32	chr2:40004400-40007000	Active TSS	Aorta	Aorta
33	chr2:40004400-40007200	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr2:40004600-40005400	Flanking Active TSS	Fetal Lung	lung
35	chr2:40004600-40005400	Flanking Active TSS	NHDF-Ad	bronchial
36	chr2:40004600-40005600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:40004600-40005600	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr2:40004600-40006000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:40004600-40006000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:40004600-40006400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:40004600-40006600	Active TSS	H1 Cell Line	embryonic stem cell
42	chr2:40004600-40006600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr2:40004600-40006600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:40004600-40006600	Active TSS	Brain Anterior Caudate	brain
45	chr2:40004600-40006600	Active TSS	Fetal Intestine Large	intestine
46	chr2:40004600-40006600	Active TSS	Fetal Thymus	thymus
47	chr2:40004600-40006600	Active TSS	Right Ventricle	heart
48	chr2:40004600-40006800	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr2:40004600-40006800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:40004600-40007000	Active TSS	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links