Variant report

Variant	rs55663439
Chromosome Location	chr15:78282749-78282750
allele	C/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	MAZ	chr15:78282688-78283240	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:78282305-78284434	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:78282659-78283628	HL-60	blood:	n/a	n/a
4	EBF1	chr15:78282541-78283379	GM12878	blood:	n/a	chr15:78282755-78282766
5	POLR2A	chr15:78282654-78283707	HL-60	blood:	n/a	n/a
6	POLR2A	chr15:78282316-78283946	SK-N-MC	brain:	n/a	n/a
7	BCL3	chr15:78282729-78283211	GM12878	blood:	n/a	n/a
8	MTA3	chr15:78282565-78283277	GM12878	blood:	n/a	n/a
9	FOXM1	chr15:78282685-78283340	GM12878	blood:	n/a	n/a
10	GABPA	chr15:78282711-78283287	HL-60	blood:	n/a	n/a
11	POU2F2	chr15:78282570-78283391	GM12878	blood:	n/a	chr15:78282985-78282997
12	TCF12	chr15:78282623-78282838	GM12878	blood:	n/a	n/a
13	PAX5	chr15:78282486-78283317	GM12878	blood:	n/a	n/a
14	STAT1	chr15:78282677-78283166	GM12878	blood:	n/a	chr15:78282987-78282999
15	POLR2A	chr15:78281867-78282946	PANC-1	pancreas:	n/a	n/a
16	TCF3	chr15:78282490-78283524	GM12878	blood:	n/a	n/a
17	EBF1	chr15:78282512-78282883	GM12878	blood:	n/a	chr15:78282755-78282766
18	EBF1	chr15:78282543-78283289	GM12878	blood:	n/a	chr15:78282755-78282766
19	TFAP2C	chr15:78282566-78283104	Hela-S3	cervix:	n/a	n/a
20	CUX1	chr15:78282659-78283162	GM12878	blood:	n/a	n/a
21	MAZ	chr15:78282744-78283110	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr15:78282439-78283835	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:78258415..78260755-chr15:78280770..78282867,2	MCF-7	breast:
2	chr15:78275999..78279475-chr15:78281569..78284408,3	MCF-7	breast:
3	chr15:78275921..78279838-chr15:78281220..78285014,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259792	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10519182	0.88[EUR][1000 genomes]
rs16969405	0.88[EUR][1000 genomes]
rs16969407	0.88[EUR][1000 genomes]
rs16969408	0.88[EUR][1000 genomes]
rs16969414	0.88[EUR][1000 genomes]
rs1985487	0.88[EUR][1000 genomes]
rs28441175	0.88[EUR][1000 genomes]
rs28451835	0.88[EUR][1000 genomes]
rs28470811	0.88[EUR][1000 genomes]
rs28491609	0.83[EUR][1000 genomes]
rs28526757	0.88[EUR][1000 genomes]
rs28674965	0.88[EUR][1000 genomes]
rs4991997	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55930913	0.88[EUR][1000 genomes]
rs57949748	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58098690	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58117418	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7167778	0.88[EUR][1000 genomes]
rs74027705	0.88[EUR][1000 genomes]
rs74027706	0.88[EUR][1000 genomes]
rs74027709	0.88[EUR][1000 genomes]
rs74029743	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74029754	0.88[EUR][1000 genomes]
rs7495105	0.89[AFR][1000 genomes]
rs7495639	0.88[EUR][1000 genomes]
rs9920647	0.88[EUR][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	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS 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	80 gene(s)	inside rSNPs	diseases
3	esv1833316	chr15:78081307-78328108	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78276000-78285200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:78276600-78282800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr15:78277600-78285600	Enhancers	Placenta	Placenta
4	chr15:78278400-78288800	Enhancers	Fetal Muscle Leg	muscle
5	chr15:78279400-78287600	Enhancers	Fetal Heart	heart
6	chr15:78279400-78287800	Enhancers	Adipose Nuclei	Adipose
7	chr15:78279400-78289800	Enhancers	Ovary	ovary
8	chr15:78279600-78283200	Weak transcription	Brain Germinal Matrix	brain
9	chr15:78279800-78282800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr15:78279800-78283400	Enhancers	Stomach Smooth Muscle	stomach
11	chr15:78279800-78289600	Weak transcription	Fetal Brain Female	brain
12	chr15:78280000-78282800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:78280000-78282800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr15:78280000-78282800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr15:78280000-78282800	Weak transcription	A549	lung
16	chr15:78280000-78283000	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr15:78280000-78284400	Enhancers	Spleen	Spleen
18	chr15:78280000-78285400	Enhancers	Fetal Thymus	thymus
19	chr15:78280000-78290400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr15:78280200-78283000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:78280200-78283000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr15:78280200-78284000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr15:78280200-78295800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:78280400-78282800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:78280400-78282800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:78280600-78284600	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr15:78280800-78283200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr15:78280800-78283400	Enhancers	Thymus	Thymus
29	chr15:78280800-78285800	Enhancers	Lung	lung
30	chr15:78280800-78286400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:78280800-78287600	Enhancers	Right Ventricle	heart
32	chr15:78281000-78285000	Enhancers	Fetal Lung	lung
33	chr15:78281000-78289600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr15:78281200-78283800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr15:78281200-78284600	Enhancers	HSMM	muscle
36	chr15:78281200-78285400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr15:78281200-78287000	Enhancers	Pancreas	Pancrea
38	chr15:78281400-78284600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:78281400-78285000	Enhancers	Duodenum Mucosa	Duodenum
40	chr15:78281600-78283600	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr15:78281800-78284400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:78281800-78287600	Enhancers	Right Atrium	heart
43	chr15:78282000-78283400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr15:78282000-78284200	Enhancers	Fetal Stomach	stomach
45	chr15:78282000-78286000	Enhancers	HSMMtube	muscle
46	chr15:78282000-78287800	Enhancers	Rectal Smooth Muscle	rectum
47	chr15:78282200-78283400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr15:78282200-78283400	Enhancers	Primary T cells from cord blood	blood
49	chr15:78282200-78283800	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr15:78282200-78284200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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