Variant report

Variant	rs11951965
Chromosome Location	chr5:115151062-115151063
allele	C/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	REST	chr5:115151061-115153120	H1-neurons	neurons:	n/a	chr5:115152626-115152639
2	ZNF263	chr5:115150963-115152852	HEK293-T-REx	kidney:	n/a	n/a
3	CTCF	chr5:115150940-115151090	GM12864	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115149403..115152060-chr5:115175796..115178394,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AP3S1-1	chr5:115150892-115151615	ENSG00000248017

Variant related genes	Relation type
CDO1	TF binding region
ENSG00000145782	Chromatin interaction
ENSG00000177879	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10058994	0.88[AMR][1000 genomes]
rs10477545	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10478261	0.96[AFR][1000 genomes]
rs10519429	0.88[AMR][1000 genomes]
rs11958544	0.83[AMR][1000 genomes]
rs11959754	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11960070	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12782	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1968365	0.88[AMR][1000 genomes]
rs4920894	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60326315	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6594908	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6865002	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73259615	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73265491	0.88[AMR][1000 genomes]
rs73267415	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73780662	0.86[EUR][1000 genomes]
rs9326975	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv949677	chr5:115104829-115496168	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115149000-115151800	Active TSS	Right Atrium	heart
2	chr5:115149200-115151200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
3	chr5:115149200-115152800	Active TSS	Aorta	Aorta
4	chr5:115149400-115151200	Flanking Bivalent TSS/Enh	Fetal Lung	lung
5	chr5:115149600-115151200	Flanking Active TSS	Brain Anterior Caudate	brain
6	chr5:115149600-115151600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:115149600-115152200	Bivalent/Poised TSS	Psoas Muscle	Psoas
8	chr5:115149800-115151400	Active TSS	Placenta	Placenta
9	chr5:115149800-115153000	Active TSS	Liver	Liver
10	chr5:115150200-115152600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:115150400-115151200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:115150400-115151200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:115150600-115151200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
14	chr5:115150600-115151200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
15	chr5:115150600-115151400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
16	chr5:115150600-115151600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:115150600-115152000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:115150600-115153000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
19	chr5:115150800-115151200	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:115150800-115151200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
21	chr5:115150800-115151200	Active TSS	Adipose Nuclei	Adipose
22	chr5:115150800-115151200	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
23	chr5:115150800-115151200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
24	chr5:115150800-115151200	Bivalent Enhancer	HepG2	liver
25	chr5:115150800-115151400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
26	chr5:115150800-115151400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
27	chr5:115150800-115151400	Flanking Active TSS	Brain Hippocampus Middle	brain
28	chr5:115150800-115151400	Flanking Bivalent TSS/Enh	NH-A	brain
29	chr5:115150800-115151600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:115150800-115151800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr5:115150800-115152000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
32	chr5:115150800-115152400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
33	chr5:115150800-115152600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
34	chr5:115150800-115152800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
35	chr5:115150800-115152800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:115150800-115152800	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr5:115150800-115153400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
38	chr5:115151000-115151200	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
39	chr5:115151000-115151200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr5:115151000-115151200	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr5:115151000-115151200	Flanking Bivalent TSS/Enh	Fetal Heart	heart
42	chr5:115151000-115151200	Enhancers	Rectal Smooth Muscle	rectum
43	chr5:115151000-115151400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
44	chr5:115151000-115151400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr5:115151000-115151400	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
46	chr5:115151000-115151400	Flanking Active TSS	Brain Substantia Nigra	brain
47	chr5:115151000-115151400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
48	chr5:115151000-115151400	Bivalent/Poised TSS	Left Ventricle	heart
49	chr5:115151000-115151400	Flanking Active TSS	Ovary	ovary
50	chr5:115151000-115151400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle

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