Variant report

Variant	rs10127937
Chromosome Location	chr1:210005821-210005822
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:210001362..210003899-chr1:210005802..210009709,4	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10218448	0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489344	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119354	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11582607	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11584081	0.95[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];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12401430	0.86[ASN][1000 genomes]
rs12403006	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12404886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[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];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2013196	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28601717	0.98[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	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41274838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4240837	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]
rs56071308	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56268268	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61820635	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6699507	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7526313	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7544804	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7546104	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs932334	0.95[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10127937	IRF6	cis	Whole Blood	GTEx
rs10127937	ETNK2	cis	cerebellum	SCAN
rs10127937	IRF6	cis	cerebellum	SCAN
rs10127937	IKBKE	cis	parietal	SCAN
rs10127937	HHAT	cis	parietal	SCAN

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	chr1:210002000-210006000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:210002000-210006000	Weak transcription	Gastric	stomach
6	chr1:210002000-210006200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:210002000-210006400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:210002000-210006600	Weak transcription	Esophagus	oesophagus
9	chr1:210002000-210006600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:210002000-210007000	Weak transcription	Colonic Mucosa	Colon
11	chr1:210002000-210007000	Weak transcription	Thymus	Thymus
12	chr1:210002000-210007200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:210002000-210011200	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr1:210002000-210015600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:210002000-210023800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:210002200-210006600	Weak transcription	Right Ventricle	heart
17	chr1:210002400-210032000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:210002600-210006600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:210003000-210006000	Weak transcription	Fetal Stomach	stomach
20	chr1:210003000-210006200	Weak transcription	Lung	lung
21	chr1:210003000-210009800	Weak transcription	Small Intestine	intestine
22	chr1:210003000-210011000	Weak transcription	Fetal Heart	heart
23	chr1:210003000-210013200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:210003200-210006600	Weak transcription	Fetal Brain Male	brain
25	chr1:210003200-210006800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:210003200-210007600	Weak transcription	Psoas Muscle	Psoas
27	chr1:210003200-210017400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:210003200-210027800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:210003200-210028600	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr1:210003200-210029400	Strong transcription	Fetal Muscle Trunk	muscle
31	chr1:210003400-210006200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr1:210003400-210028000	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr1:210003400-210028400	Strong transcription	Primary B cells from peripheral blood	blood
34	chr1:210003600-210012200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:210003600-210028000	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:210003800-210006400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:210003800-210011800	Strong transcription	A549	lung
38	chr1:210003800-210013200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:210003800-210028000	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:210003800-210028200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:210003800-210028400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:210004000-210012000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:210004000-210015800	Genic enhancers	NHDF-Ad	bronchial
44	chr1:210004000-210019000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
45	chr1:210004000-210019000	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr1:210004000-210021400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:210004000-210027600	Strong transcription	K562	blood
48	chr1:210004000-210027800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:210004000-210028000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:210004000-210028000	Strong transcription	Fetal Thymus	thymus

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