Variant report

Variant	rs3753510
Chromosome Location	chr1:210011536-210011537
allele	A/G
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	POLR2A	chr1:210010382-210011568	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
DIEXF	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10127937	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10218448	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489344	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119354	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11582607	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	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11810091	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	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	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2013196	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]
rs3753513	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766615	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]
rs4240837	1.00[AFR][1000 genomes];1.00[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	0.81[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3753510	IRF6	cis	cerebellar cortex	BrainEAC
rs3753510	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	chr1:210001800-210025000	Weak transcription	Stomach Mucosa	stomach
2	chr1:210001800-210034000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:210002000-210015600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:210002000-210023800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:210002400-210032000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:210003000-210013200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:210003200-210017400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:210003200-210027800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:210003200-210028600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr1:210003200-210029400	Strong transcription	Fetal Muscle Trunk	muscle
11	chr1:210003400-210028000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr1:210003400-210028400	Strong transcription	Primary B cells from peripheral blood	blood
13	chr1:210003600-210012200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:210003600-210028000	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:210003800-210011800	Strong transcription	A549	lung
16	chr1:210003800-210013200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:210003800-210028000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:210003800-210028200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:210003800-210028400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:210004000-210012000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:210004000-210015800	Genic enhancers	NHDF-Ad	bronchial
22	chr1:210004000-210019000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
23	chr1:210004000-210019000	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:210004000-210021400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:210004000-210027600	Strong transcription	K562	blood
26	chr1:210004000-210027800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:210004000-210028000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:210004000-210028000	Strong transcription	Fetal Thymus	thymus
29	chr1:210004000-210028200	Strong transcription	Duodenum Mucosa	Duodenum
30	chr1:210004000-210030800	Strong transcription	Primary B cells from cord blood	blood
31	chr1:210004200-210013000	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:210004200-210013200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:210004200-210013200	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr1:210004200-210017600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:210004200-210018200	Strong transcription	Brain Substantia Nigra	brain
36	chr1:210004200-210018600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:210004200-210018600	Strong transcription	Fetal Lung	lung
38	chr1:210004200-210018600	Strong transcription	Left Ventricle	heart
39	chr1:210004200-210018800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:210004200-210018800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:210004200-210019000	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr1:210004200-210019000	Strong transcription	Brain Anterior Caudate	brain
43	chr1:210004200-210019400	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr1:210004200-210019400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr1:210004200-210020200	Strong transcription	Brain Angular Gyrus	brain
46	chr1:210004200-210020200	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:210004200-210022000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:210004200-210027600	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr1:210004200-210027600	Strong transcription	Primary hematopoietic stem cells	blood
50	chr1:210004200-210027600	Strong transcription	Rectal Mucosa Donor 31	rectum

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