Variant report

Variant	rs11959669
Chromosome Location	chr5:115152891-115152892
allele	A/T
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	CHD1	chr5:115152141-115152996	IMR90	lung:	n/a	n/a
3	POLR2A	chr5:115151132-115152960	H1-neurons	neurons:	n/a	n/a
4	YY1	chr5:115151599-115152915	H1-hESC	embryonic stem cell:	n/a	chr5:115151779-115151790 chr5:115152458-115152467 chr5:115151884-115151898 chr5:115151889-115151898
5	POLR2A	chr5:115151822-115152891	HepG2	liver:	n/a	n/a
6	TAF1	chr5:115151500-115152950	H1-neurons	neurons:	n/a	n/a
7	CREB1	chr5:115151989-115152956	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115147173..115150653-chr5:115151450..115154733,4	K562	blood:

Variant related genes	Relation type
CDO1	TF binding region
ENSG00000129596	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10036657	1.00[EUR][1000 genomes]
rs10052079	1.00[EUR][1000 genomes]
rs10054972	1.00[EUR][1000 genomes]
rs10058994	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10059199	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10067222	1.00[EUR][1000 genomes]
rs10070325	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10074061	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10074066	1.00[EUR][1000 genomes]
rs10075816	1.00[EUR][1000 genomes]
rs10477545	0.89[AMR][1000 genomes]
rs10478262	1.00[EUR][1000 genomes]
rs10519428	1.00[EUR][1000 genomes]
rs10519429	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11958544	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11959754	0.85[AMR][1000 genomes]
rs11960070	0.89[AMR][1000 genomes]
rs17138236	1.00[EUR][1000 genomes]
rs1968365	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28420368	1.00[EUR][1000 genomes]
rs4920893	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4921029	1.00[EUR][1000 genomes]
rs4921030	1.00[EUR][1000 genomes]
rs6594908	0.85[AMR][1000 genomes]
rs6861998	1.00[EUR][1000 genomes]
rs6865002	0.89[AMR][1000 genomes]
rs6872587	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6875708	1.00[EUR][1000 genomes]
rs73257802	1.00[EUR][1000 genomes]
rs73265480	1.00[EUR][1000 genomes]
rs73265491	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73265501	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73267415	0.89[AMR][1000 genomes]
rs73780683	1.00[EUR][1000 genomes]
rs9326975	1.00[EUR][1000 genomes]
rs9654524	1.00[EUR][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:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115149800-115153000	Active TSS	Liver	Liver
2	chr5:115150600-115153000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr5:115150800-115153400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr5:115151000-115153000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:115151000-115153200	Active TSS	Fetal Brain Male	brain
6	chr5:115151000-115153200	Active TSS	Fetal Brain Female	brain
7	chr5:115151000-115153200	Active TSS	Fetal Kidney	kidney
8	chr5:115151200-115153000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr5:115151200-115153000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr5:115151200-115153000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
11	chr5:115151200-115153000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
12	chr5:115151200-115153200	Active TSS	Brain Germinal Matrix	brain
13	chr5:115151200-115153200	Bivalent/Poised TSS	Fetal Lung	lung
14	chr5:115151400-115153000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:115151400-115153000	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
16	chr5:115151400-115153000	Active TSS	Ovary	ovary
17	chr5:115151600-115153000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:115151600-115153000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:115151600-115153000	Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr5:115151600-115153000	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
21	chr5:115151600-115153000	Bivalent/Poised TSS	Placenta	Placenta
22	chr5:115151600-115153000	Bivalent/Poised TSS	Fetal Stomach	stomach
23	chr5:115151600-115153200	Active TSS	Brain Anterior Caudate	brain
24	chr5:115151800-115153000	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:115151800-115153000	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr5:115151800-115153000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
27	chr5:115152000-115153200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:115152200-115153200	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr5:115152400-115153000	Active TSS	Right Atrium	heart
30	chr5:115152400-115153000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
31	chr5:115152400-115153400	Active TSS	Brain Cingulate Gyrus	brain
32	chr5:115152600-115153000	Active TSS	H1 Cell Line	embryonic stem cell
33	chr5:115152600-115153000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:115152600-115153000	Active TSS	Adipose Nuclei	Adipose
35	chr5:115152800-115153000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr5:115152800-115153000	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr5:115152800-115153000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:115152800-115153000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:115152800-115153000	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:115152800-115153000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr5:115152800-115153000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr5:115152800-115153000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
43	chr5:115152800-115153000	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
44	chr5:115152800-115153200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr5:115152800-115153200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr5:115152800-115154200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr5:115152800-115154200	Weak transcription	Brain Angular Gyrus	brain
48	chr5:115152800-115154200	Weak transcription	Brain Hippocampus Middle	brain
49	chr5:115152800-115154200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr5:115152800-115154400	Weak transcription	Brain Substantia Nigra	brain

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