Variant report

Variant	rs11577282
Chromosome Location	chr1:226287622-226287623
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226286017..226288107-chr1:226288751..226292148,3	K562	blood:
2	chr1:226285884..226288013-chr1:226296594..226298367,3	K562	blood:
3	chr1:226281557..226283150-chr1:226286865..226289299,2	MCF-7	breast:
4	chr1:226248606..226253173-chr1:226284657..226288071,4	MCF-7	breast:
5	chr1:226249583..226251274-chr1:226286013..226287713,2	K562	blood:
6	chr1:226286961..226289894-chr1:226295202..226296764,2	MCF-7	breast:
7	chr1:226280306..226283507-chr1:226285698..226289497,4	K562	blood:
8	chr1:226280924..226283749-chr1:226285307..226289660,6	K562	blood:
9	chr1:226286017..226288107-chr1:226288751..226291625,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163041	Chromatin interaction
ENSG00000272562	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10915934	0.91[EUR][1000 genomes]
rs10915936	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12069333	0.84[ASN][1000 genomes]
rs12117683	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12117819	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12121071	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12144544	0.87[EUR][1000 genomes]
rs1219671	0.90[JPT][hapmap]
rs1355391	0.91[CEU][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs1877155	0.90[JPT][hapmap]
rs3892709	0.90[JPT][hapmap]
rs6693755	0.87[EUR][1000 genomes]
rs7515023	0.95[CEU][hapmap];0.87[CHB][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs7552463	0.88[EUR][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	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
3	esv1792510	chr1:226277560-226323824	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11577282	CNIH4	cis	parietal	SCAN
rs11577282	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx
rs11577282	H3F3A	cis	Muscle Skeletal	GTEx
rs11577282	H3F3A	cis	Artery Aorta	GTEx
rs11577282	H3F3A	cis	Adipose Subcutaneous	GTEx
rs11577282	H3F3A	cis	Esophagus Mucosa	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226271800-226288000	Weak transcription	Right Atrium	heart
2	chr1:226271800-226288400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:226272000-226287800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:226272000-226288200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:226281200-226295000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:226284800-226288000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:226286200-226287800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:226286200-226287800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:226286200-226287800	Weak transcription	HSMM	muscle
10	chr1:226286200-226287800	Weak transcription	NH-A	brain
11	chr1:226286200-226287800	Weak transcription	NHDF-Ad	bronchial
12	chr1:226286200-226287800	Enhancers	NHEK	skin
13	chr1:226286200-226288000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:226286200-226288000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:226286200-226288400	Weak transcription	Esophagus	oesophagus
16	chr1:226286200-226297200	Weak transcription	Hela-S3	cervix
17	chr1:226286600-226288200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:226286600-226291800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:226287000-226288000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:226287000-226288200	Weak transcription	HMEC	breast
21	chr1:226287200-226287800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:226287200-226288400	Weak transcription	K562	blood
23	chr1:226287400-226287800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
24	chr1:226287400-226287800	Enhancers	Brain Hippocampus Middle	brain
25	chr1:226287600-226287800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:226287600-226287800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:226287600-226287800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:226287600-226287800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:226287600-226287800	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr1:226287600-226287800	Enhancers	Brain Cingulate Gyrus	brain
31	chr1:226287600-226287800	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr1:226287600-226287800	Enhancers	Fetal Kidney	kidney
33	chr1:226287600-226287800	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr1:226287600-226288000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr1:226287600-226288000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:226287600-226288000	Enhancers	Brain Substantia Nigra	brain
37	chr1:226287600-226288000	Bivalent Enhancer	HepG2	liver
38	chr1:226287600-226288600	Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr1:226287600-226289000	Flanking Active TSS	GM12878-XiMat	blood

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