Variant report

Variant	rs4240837
Chromosome Location	chr1:210006371-210006372
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	chr1:210005828..210008721-chr1:210008768..210010506,3	MCF-7	breast:
2	chr1:210001362..210003899-chr1:210005802..210009709,4	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10127937	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10218448	0.84[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489344	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119354	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11582607	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11584081	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590807	1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11810091	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12401430	0.86[ASN][1000 genomes]
rs12403006	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12404886	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17317580	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17389541	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2013196	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28601717	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34743335	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3753510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753513	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766615	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41274838	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56071308	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56268268	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61820635	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6699507	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7526313	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7544804	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7546104	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs932334	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4240837	IRF6	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210001800-210010200	Weak transcription	Spleen	Spleen
2	chr1:210001800-210025000	Weak transcription	Stomach Mucosa	stomach
3	chr1:210001800-210034000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:210002000-210006400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:210002000-210006600	Weak transcription	Esophagus	oesophagus
6	chr1:210002000-210006600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:210002000-210007000	Weak transcription	Colonic Mucosa	Colon
8	chr1:210002000-210007000	Weak transcription	Thymus	Thymus
9	chr1:210002000-210007200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:210002000-210011200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:210002000-210015600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:210002000-210023800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:210002200-210006600	Weak transcription	Right Ventricle	heart
14	chr1:210002400-210032000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:210002600-210006600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:210003000-210009800	Weak transcription	Small Intestine	intestine
17	chr1:210003000-210011000	Weak transcription	Fetal Heart	heart
18	chr1:210003000-210013200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:210003200-210006600	Weak transcription	Fetal Brain Male	brain
20	chr1:210003200-210006800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:210003200-210007600	Weak transcription	Psoas Muscle	Psoas
22	chr1:210003200-210017400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:210003200-210027800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:210003200-210028600	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr1:210003200-210029400	Strong transcription	Fetal Muscle Trunk	muscle
26	chr1:210003400-210028000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr1:210003400-210028400	Strong transcription	Primary B cells from peripheral blood	blood
28	chr1:210003600-210012200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:210003600-210028000	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:210003800-210006400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:210003800-210011800	Strong transcription	A549	lung
32	chr1:210003800-210013200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:210003800-210028000	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:210003800-210028200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:210003800-210028400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:210004000-210012000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:210004000-210015800	Genic enhancers	NHDF-Ad	bronchial
38	chr1:210004000-210019000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
39	chr1:210004000-210019000	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:210004000-210021400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:210004000-210027600	Strong transcription	K562	blood
42	chr1:210004000-210027800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:210004000-210028000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:210004000-210028000	Strong transcription	Fetal Thymus	thymus
45	chr1:210004000-210028200	Strong transcription	Duodenum Mucosa	Duodenum
46	chr1:210004000-210030800	Strong transcription	Primary B cells from cord blood	blood
47	chr1:210004200-210006400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:210004200-210007200	Genic enhancers	NHLF	lung
49	chr1:210004200-210008800	Strong transcription	HepG2	liver
50	chr1:210004200-210009000	Strong transcription	Colon Smooth Muscle	Colon

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