Variant report

Variant	rs55803223
Chromosome Location	chr4:151095618-151095619
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	chr4:151094963-151095712	HUVEC	blood vessel:	n/a	n/a
2	REST	chr4:151094334-151095800	H1-neurons	neurons:	n/a	chr4:151095606-151095624
3	REST	chr4:151094197-151095930	H1-neurons	neurons:	n/a	chr4:151095606-151095624

Variant related genes	Relation type
DCLK2	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1160433	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11737192	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3922818	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4346630	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4513543	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56141146	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60467236	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7340876	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7674585	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][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	nsv1026797	chr4:150246932-151217137	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv932022	chr4:150831733-151419552	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1032689	chr4:150971003-151316856	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv537300	chr4:150971003-151316856	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv3412514	chr4:151095502-151097400	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55803223	RP11-372K14.2	cis	Nerve Tibial	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151045200-151099000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:151081400-151096600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr4:151085400-151097400	Weak transcription	Ovary	ovary
4	chr4:151089200-151097000	Weak transcription	Aorta	Aorta
5	chr4:151091600-151104800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr4:151092000-151097000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:151092200-151096800	Weak transcription	NHDF-Ad	bronchial
8	chr4:151093000-151096800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:151094000-151095800	Enhancers	HSMMtube	muscle
10	chr4:151094200-151095800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:151094200-151095800	Enhancers	Brain Hippocampus Middle	brain
12	chr4:151094200-151096000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:151094200-151096000	Enhancers	Fetal Brain Male	brain
14	chr4:151094200-151096000	Enhancers	Left Ventricle	heart
15	chr4:151094200-151098200	Enhancers	Fetal Muscle Leg	muscle
16	chr4:151094400-151095800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:151094800-151097400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:151095000-151097000	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:151095000-151097200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:151095000-151097200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:151095200-151096800	Weak transcription	Fetal Kidney	kidney
22	chr4:151095200-151097200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:151095200-151097400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:151095200-151097400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr4:151095400-151095800	Active TSS	Adipose Nuclei	Adipose
26	chr4:151095400-151096000	Enhancers	Brain Germinal Matrix	brain
27	chr4:151095400-151096000	Enhancers	HUVEC	blood vessel
28	chr4:151095400-151096400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr4:151095400-151096600	Weak transcription	Fetal Stomach	stomach
30	chr4:151095400-151096600	Weak transcription	Lung	lung
31	chr4:151095400-151096600	Weak transcription	Right Ventricle	heart
32	chr4:151095400-151097000	Weak transcription	Pancreas	Pancrea
33	chr4:151095400-151097200	Weak transcription	HSMM	muscle
34	chr4:151095400-151097400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:151095400-151097400	Weak transcription	Right Atrium	heart
36	chr4:151095400-151098000	Enhancers	Brain Anterior Caudate	brain
37	chr4:151095400-151100000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:151095400-151101400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr4:151095600-151096000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:151095600-151096600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:151095600-151096800	Enhancers	Fetal Heart	heart
42	chr4:151095600-151097000	Weak transcription	Brain Angular Gyrus	brain
43	chr4:151095600-151097000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr4:151095600-151097000	Weak transcription	Fetal Brain Female	brain
45	chr4:151095600-151097200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr4:151095600-151097200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr4:151095600-151097200	Weak transcription	Fetal Lung	lung
48	chr4:151095600-151097200	Weak transcription	Osteobl	bone
49	chr4:151095600-151097400	Weak transcription	NH-A	brain
50	chr4:151095600-151097400	Weak transcription	NHLF	lung

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