Variant report

Variant	rs2540226
Chromosome Location	chr2:39959060-39959061
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39949939..39952717-chr2:39956510..39959520,3	K562	blood:
2	chr2:39956511..39959313-chr2:39963423..39966222,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10174709	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10206408	0.82[ASN][1000 genomes]
rs10207589	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs10211306	0.84[EUR][1000 genomes]
rs1035138	0.81[ASN][1000 genomes]
rs1035139	0.81[ASN][1000 genomes]
rs11124691	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11124693	0.88[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs11684302	0.81[CEU][hapmap]
rs12470473	0.84[CEU][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12617624	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12623462	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12623545	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12624217	0.81[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs12712653	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13026313	0.84[CEU][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13425906	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1548877	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17478972	0.80[CEU][hapmap]
rs1861243	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1861258	0.81[CEU][hapmap]
rs1986876	0.86[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs2041735	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2058620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2110656	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2160198	0.82[CHB][hapmap]
rs2192685	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs2215958	0.83[EUR][1000 genomes]
rs2373688	0.86[ASN][1000 genomes]
rs2373689	0.84[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2540227	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2540228	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2540229	0.81[GIH][hapmap];0.83[EUR][1000 genomes]
rs2716704	0.83[ASN][1000 genomes]
rs2716727	0.93[ASN][1000 genomes]
rs2716729	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2716730	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3732121	0.93[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3732122	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3815510	0.82[JPT][hapmap]
rs4670955	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4670956	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4670957	0.85[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs4670958	0.85[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs4670959	0.81[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs56721088	0.81[EUR][1000 genomes]
rs59756273	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6544242	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6719179	0.86[CHB][hapmap];0.93[CHD][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs6722610	0.92[CEU][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs6731026	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6731450	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6747842	0.93[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs6750252	0.94[ASN][1000 genomes]
rs6758453	0.93[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs727376	0.81[ASN][1000 genomes]
rs7560642	0.88[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7565954	0.93[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs7581406	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7590912	0.80[GIH][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs7591296	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7591347	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8265	0.89[CEU][hapmap];0.83[MEX][hapmap];0.92[EUR][1000 genomes]
rs917960	0.84[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs917961	0.82[JPT][hapmap]
rs917962	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs917963	0.92[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9309042	0.81[ASN][1000 genomes]
rs962262	0.89[CEU][hapmap];0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs997976	0.84[CEU][hapmap];0.93[CHB][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

Variant related diseases (count:1)

Disease	PMID	Source
Personality dimensions	18957941	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2540226	THUMPD2	cis	parietal	SCAN
rs2540226	THUMPD2	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39942000-39963000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr2:39944400-39976600	Weak transcription	Fetal Brain Male	brain
3	chr2:39946800-39959600	Weak transcription	Brain Germinal Matrix	brain
4	chr2:39947800-39959800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:39948200-39961200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr2:39948800-39959600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:39949000-39960400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:39951000-39959400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:39951000-39963600	Weak transcription	Pancreas	Pancrea
10	chr2:39951000-39964800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:39951200-39964800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:39951400-39960200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:39951400-39961400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:39951400-39961800	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:39951400-39962000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:39951400-39963800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr2:39952000-39964800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:39952200-39960200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr2:39952400-39962400	Weak transcription	Spleen	Spleen
20	chr2:39952600-39962600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:39952800-39960200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:39952800-39962400	Weak transcription	Fetal Kidney	kidney
23	chr2:39952800-39962600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:39953000-39959400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:39953200-39962400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr2:39953600-39959400	Weak transcription	Esophagus	oesophagus
27	chr2:39954400-39959600	Weak transcription	HepG2	liver
28	chr2:39954400-39960000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:39954600-39960000	Weak transcription	K562	blood
30	chr2:39954800-39959800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:39955000-39959400	Weak transcription	A549	lung
32	chr2:39955200-39959200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:39955800-39960400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr2:39956000-39959400	Weak transcription	Primary B cells from cord blood	blood
35	chr2:39956000-39962800	Weak transcription	HUVEC	blood vessel
36	chr2:39956200-39959600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:39956200-39960400	Weak transcription	GM12878-XiMat	blood
38	chr2:39956200-39962200	Weak transcription	Adipose Nuclei	Adipose
39	chr2:39956200-39966400	Weak transcription	Small Intestine	intestine
40	chr2:39956400-39959200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:39956400-39959400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:39956400-39959400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:39956400-39959400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:39956400-39959600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr2:39956400-39962600	Weak transcription	Placenta	Placenta
46	chr2:39956600-39959400	Weak transcription	NHDF-Ad	bronchial
47	chr2:39956600-39959600	Weak transcription	Dnd41	blood
48	chr2:39956600-39960400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr2:39956600-39962000	Weak transcription	Primary B cells from peripheral blood	blood
50	chr2:39956600-39962000	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links