Variant report

Variant	rs12404886
Chromosome Location	chr1:210001543-210001544
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209999396..210002885-chr1:210546190..210548808,3	K562	blood:
2	chr1:209977871..209984485-chr1:209998424..210002427,6	K562	blood:
3	chr1:209977871..209981214-chr1:209999703..210002866,6	K562	blood:
4	chr1:210001362..210003899-chr1:210005802..210009709,4	K562	blood:
5	chr1:210000759..210001556-chr13:31039833..31040722,2	NB4	blood:

Variant related genes	Relation type
ENSG00000117595	Chromatin interaction
ENSG00000189403	Chromatin interaction
ENSG00000200972	Chromatin interaction

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];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]
rs10218448	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[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[JPT][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119354	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11582607	1.00[CHB][hapmap];1.00[JPT][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	0.88[CEU][hapmap];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];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]
rs17317580	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17389541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2013196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28601717	0.97[AFR][1000 genomes];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[JPT][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[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41274838	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4240837	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]
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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12404886	IRF6	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210000400-210002400	Active TSS	A549	lung
2	chr1:210000600-210002000	Active TSS	Colonic Mucosa	Colon
3	chr1:210000600-210002200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:210000600-210002400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:210000600-210002400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:210000600-210002400	Active TSS	Right Atrium	heart
7	chr1:210000600-210002600	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr1:210000600-210002600	Active TSS	K562	blood
9	chr1:210000800-210001600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:210000800-210001600	Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr1:210000800-210001800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr1:210000800-210002000	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr1:210000800-210002000	Active TSS	H1 Cell Line	embryonic stem cell
14	chr1:210000800-210002000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:210000800-210002000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:210000800-210002000	Active TSS	H9 Cell Line	embryonic stem cell
17	chr1:210000800-210002000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:210000800-210002000	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr1:210000800-210002000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:210000800-210002000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr1:210000800-210002000	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr1:210000800-210002000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:210000800-210002000	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr1:210000800-210002000	Active TSS	Aorta	Aorta
25	chr1:210000800-210002000	Active TSS	Brain Angular Gyrus	brain
26	chr1:210000800-210002000	Active TSS	Brain Anterior Caudate	brain
27	chr1:210000800-210002000	Active TSS	Brain Cingulate Gyrus	brain
28	chr1:210000800-210002000	Active TSS	Brain Hippocampus Middle	brain
29	chr1:210000800-210002000	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr1:210000800-210002000	Active TSS	Brain Substantia Nigra	brain
31	chr1:210000800-210002000	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr1:210000800-210002000	Active TSS	Esophagus	oesophagus
33	chr1:210000800-210002000	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr1:210000800-210002000	Active TSS	Fetal Stomach	stomach
35	chr1:210000800-210002000	Active TSS	Rectal Smooth Muscle	rectum
36	chr1:210000800-210002000	Active TSS	Thymus	Thymus
37	chr1:210000800-210002000	Active TSS	NHDF-Ad	bronchial
38	chr1:210000800-210002200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:210000800-210002200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:210000800-210002200	Active TSS	Brain Germinal Matrix	brain
41	chr1:210000800-210002200	Active TSS	Ovary	ovary
42	chr1:210000800-210002200	Active TSS	Right Ventricle	heart
43	chr1:210000800-210002400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:210000800-210002400	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr1:210000800-210002400	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr1:210000800-210002400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:210000800-210002400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:210000800-210002400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:210000800-210002400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:210000800-210002400	Active TSS	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links