Variant report

Variant	rs4523509
Chromosome Location	chr1:154452100-154452101
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	YY1	chr1:154452094-154452661	SK-N-SH	brain:	n/a	n/a
2	CHD1	chr1:154451948-154452866	IMR90	lung:	n/a	n/a
3	RAD21	chr1:154452097-154452862	A549	lung:	n/a	n/a
4	CTCF	chr1:154452022-154453006	HCT-116	colon:	n/a	n/a
5	CTCF	chr1:154452041-154452896	SK-N-SH	brain:	n/a	n/a
6	RAD21	chr1:154451828-154453056	SK-N-SH	brain:	n/a	n/a
7	RAD21	chr1:154452076-154452957	HCT-116	colon:	n/a	n/a
8	CTCF	chr1:154451926-154452927	A549	lung:	n/a	n/a
9	MAFK	chr1:154452072-154452677	Hela-S3	cervix:	n/a	chr1:154452378-154452393
10	SRF	chr1:154452015-154452857	HCT-116	colon:	n/a	chr1:154452391-154452409
11	SRF	chr1:154452098-154452811	HCT-116	colon:	n/a	chr1:154452391-154452409
12	MAFK	chr1:154452066-154453029	GM12878	blood:	n/a	chr1:154452378-154452393
13	RAD21	chr1:154452056-154452913	HCT-116	colon:	n/a	n/a
14	RFX5	chr1:154451417-154454216	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154450895..154452428-chr1:154521385..154523605,2	K562	blood:
2	chr1:154301762..154302404-chr1:154451842..154452428,2	MCF-7	breast:
3	chr1:154450828..154453659-chr1:154529713..154531945,2	MCF-7	breast:
4	chr1:154450305..154454149-chr1:154524357..154527096,3	MCF-7	breast:

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	SHE	hsa-miR-124-3p	chr1:154452083-154452102

Variant related genes	Relation type
ENSG00000273110	TF binding region
ENSG00000160714	Chromatin interaction
ENSG00000229780	Chromatin interaction
SHE	miRNA target site

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs4845633	0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7525993	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7529744	0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][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	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154427800-154464800	Weak transcription	Ovary	ovary
2	chr1:154438400-154457800	Weak transcription	Pancreas	Pancrea
3	chr1:154438400-154458400	Weak transcription	Gastric	stomach
4	chr1:154438400-154463400	Weak transcription	Esophagus	oesophagus
5	chr1:154438800-154454000	Weak transcription	Psoas Muscle	Psoas
6	chr1:154439400-154457600	Weak transcription	Placenta	Placenta
7	chr1:154440000-154452800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:154440000-154458200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:154441600-154465200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:154442400-154455200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:154442400-154455800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:154442800-154452200	Weak transcription	Brain Anterior Caudate	brain
13	chr1:154442800-154452600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr1:154442800-154455600	Weak transcription	Left Ventricle	heart
15	chr1:154442800-154456400	Weak transcription	Spleen	Spleen
16	chr1:154443000-154452400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:154443000-154456400	Weak transcription	Right Ventricle	heart
18	chr1:154443000-154464400	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:154447000-154452200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr1:154447600-154452200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:154447600-154452200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:154447600-154452200	Weak transcription	NHDF-Ad	bronchial
23	chr1:154447600-154455800	Weak transcription	Lung	lung
24	chr1:154447800-154458400	Weak transcription	Brain Angular Gyrus	brain
25	chr1:154448400-154452400	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:154448400-154452600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:154448600-154458200	Weak transcription	Brain Substantia Nigra	brain
28	chr1:154448800-154452200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:154449800-154452200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:154449800-154456400	Weak transcription	Hela-S3	cervix
31	chr1:154450000-154454000	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr1:154450000-154457000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:154450000-154462400	Weak transcription	Colonic Mucosa	Colon
34	chr1:154450200-154456600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:154450400-154452400	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr1:154450400-154452400	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr1:154450400-154452400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:154450400-154453000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:154450600-154452400	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr1:154450600-154452400	Enhancers	GM12878-XiMat	blood
41	chr1:154450600-154452600	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr1:154450600-154452600	Enhancers	Fetal Thymus	thymus
43	chr1:154450600-154452800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr1:154450600-154452800	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr1:154450800-154452200	Weak transcription	Fetal Intestine Small	intestine
46	chr1:154450800-154452400	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr1:154450800-154453000	Enhancers	A549	lung
48	chr1:154451000-154452400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:154451000-154452400	Enhancers	HMEC	breast
50	chr1:154451200-154452200	Weak transcription	Duodenum Mucosa	Duodenum

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