Variant report

Variant	rs12594316
Chromosome Location	chr15:74894061-74894062
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL3	chr15:74894049-74894342	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:74893062..74896210-chr15:74919628..74922428,3	K562	blood:
2	chr15:74891163..74893467-chr15:74893596..74895699,2	K562	blood:
3	chr15:74665982..74668403-chr15:74893258..74895614,2	MCF-7	breast:
4	chr15:74892526..74894562-chr15:74919446..74922428,2	K562	blood:
5	chr15:74893262..74895445-chr15:74915214..74917885,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLK3-1	chr15:74893933-74894236	NONHSAT047251

No data

Variant related genes	Relation type
CLK3	TF binding region
ENSG00000179335	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12591497	0.87[AMR][1000 genomes]
rs12593898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs12594105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12594462	1.00[CEU][hapmap]
rs16953854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs16969770	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs1799814	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs3184088	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3747478	1.00[CEU][hapmap]
rs58386058	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58723548	0.82[ASN][1000 genomes]
rs58747223	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59825838	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60494023	0.82[AMR][1000 genomes]
rs8023274	1.00[CEU][hapmap]
rs8031284	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1809847	chr15:74734500-74948063	Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	esv1812223	chr15:74869438-74948063	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv904379	chr15:74869438-75027880	Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	esv1814078	chr15:74884447-74948063	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv457204	chr15:74885091-74948063	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv569991	chr15:74885091-74948063	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv542434	chr15:74885329-74929552	Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1047943	chr15:74885329-74940857	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	nsv817698	chr15:74889163-75019449	Genic enhancers Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74891200-74894200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:74891200-74899200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:74891400-74896600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr15:74891400-74898000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:74891400-74903400	Weak transcription	HMEC	breast
6	chr15:74891600-74896800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr15:74891600-74907200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr15:74891800-74895400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:74891800-74896800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:74892000-74895800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:74892000-74896800	Weak transcription	NHLF	lung
12	chr15:74892000-74897400	Weak transcription	Brain Hippocampus Middle	brain
13	chr15:74892000-74902400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:74892200-74894400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr15:74892200-74894400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:74892200-74894600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:74892200-74895600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr15:74892200-74897000	Weak transcription	Fetal Intestine Large	intestine
19	chr15:74892200-74898200	Weak transcription	Fetal Kidney	kidney
20	chr15:74892200-74902600	Weak transcription	Right Atrium	heart
21	chr15:74892200-74906000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:74892200-74906600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:74892400-74894200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr15:74892400-74894200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:74892400-74894400	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr15:74892400-74894800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:74892400-74895000	Weak transcription	HepG2	liver
28	chr15:74892400-74895200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:74892400-74895200	Strong transcription	Fetal Intestine Small	intestine
30	chr15:74892400-74895400	Weak transcription	Stomach Mucosa	stomach
31	chr15:74892400-74895600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr15:74892400-74895800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr15:74892400-74898800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:74892400-74902600	Weak transcription	Ovary	ovary
35	chr15:74892400-74906000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr15:74892400-74906400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr15:74892400-74906600	Weak transcription	Primary T cells from cord blood	blood
38	chr15:74892400-74906600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:74892600-74894600	Strong transcription	Fetal Stomach	stomach
40	chr15:74892600-74895200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr15:74892600-74902600	Weak transcription	Spleen	Spleen
42	chr15:74892600-74902800	Weak transcription	Lung	lung
43	chr15:74893000-74906600	Weak transcription	Fetal Brain Female	brain
44	chr15:74893200-74894600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr15:74893200-74896000	Weak transcription	Placenta	Placenta
46	chr15:74893200-74906200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr15:74893400-74894800	Weak transcription	Right Ventricle	heart
48	chr15:74893400-74895400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr15:74893400-74902400	Weak transcription	Left Ventricle	heart
50	chr15:74893600-74894400	Weak transcription	Fetal Muscle Trunk	muscle

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