Variant report

Variant	rs5754399
Chromosome Location	chr22:33453422-33453423
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	22:32846948-32860159..22:33452523-33459358	Hela-S3	cervix:
2	22:32360288-32405313..22:33452523-33459358	H1-hESC	embryonic stem cell:	embryo
3	22:33030812-33041554..22:33452523-33459358	GM12878	blood:

Variant related genes	Relation type
ENSG00000230866	Chromatin interaction
ENSG00000184459	Chromatin interaction
ENSG00000240647	Chromatin interaction
ENSG00000251890	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1981469	0.85[EUR][1000 genomes]
rs57330381	0.85[EUR][1000 genomes]
rs5749551	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5749552	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5754391	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8142672	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs929040	0.83[EUR][1000 genomes]
rs9306273	0.85[EUR][1000 genomes]
rs9621631	0.90[CEU][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531568	chr22:33336868-33480272	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv531587	chr22:33346710-33809338	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv948523	chr22:33414164-34098417	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1067068	chr22:33452180-33851033	Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
5	esv3390652	chr22:33452977-33455825	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33449400-33453600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
2	chr22:33450800-33454600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr22:33451200-33454800	Bivalent/Poised TSS	Brain Angular Gyrus	brain
4	chr22:33452200-33454800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
5	chr22:33452400-33453800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr22:33452600-33454600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
7	chr22:33452800-33454000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr22:33452800-33454000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr22:33452800-33454000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
10	chr22:33452800-33454200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr22:33452800-33454800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
12	chr22:33453000-33453600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr22:33453000-33453800	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
14	chr22:33453000-33454000	Bivalent/Poised TSS	Fetal Brain Female	brain
15	chr22:33453000-33454400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr22:33453200-33453600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
17	chr22:33453200-33453600	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr22:33453200-33453600	Bivalent Enhancer	Brain Germinal Matrix	brain
19	chr22:33453200-33453800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
20	chr22:33453200-33453800	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr22:33453200-33454000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
22	chr22:33453400-33453600	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr22:33453400-33453600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr22:33453400-33453600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr22:33453400-33453600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr22:33453400-33453600	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
27	chr22:33453400-33453600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
28	chr22:33453400-33453600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
29	chr22:33453400-33453800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr22:33453400-33453800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
31	chr22:33453400-33453800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
32	chr22:33453400-33453800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr22:33453400-33453800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
34	chr22:33453400-33453800	Flanking Bivalent TSS/Enh	HepG2	liver
35	chr22:33453400-33454000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
36	chr22:33453400-33454000	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
37	chr22:33453400-33454000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr22:33453400-33454000	Bivalent Enhancer	Adipose Nuclei	Adipose
39	chr22:33453400-33454000	Bivalent Enhancer	Placenta	Placenta
40	chr22:33453400-33454200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
41	chr22:33453400-33454800	Bivalent Enhancer	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links