Variant report

Variant	rs28416908
Chromosome Location	chr15:74504889-74504890
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr15:74504803-74505199	GM12878	blood:	n/a	n/a
2	RUNX3	chr15:74504581-74505252	GM12878	blood:	n/a	n/a
3	CTCF	chr15:74504866-74504900	Kidney_OC	kidney:	n/a	n/a
4	WRNIP1	chr15:74504760-74505061	GM12878	blood:	n/a	n/a
5	RAD21	chr15:74504886-74505171	GM12878	blood:	n/a	n/a
6	TBL1XR1	chr15:74504871-74505138	GM12878	blood:	n/a	n/a
7	RUNX3	chr15:74504719-74505310	GM12878	blood:	n/a	n/a
8	MTA3	chr15:74504677-74505291	GM12878	blood:	n/a	n/a
9	FOXM1	chr15:74504813-74505254	GM12878	blood:	n/a	n/a
10	RAD21	chr15:74504591-74505024	H1-hESC	embryonic stem cell:	n/a	n/a
11	MTA3	chr15:74504415-74505189	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:74504672..74507489-chr15:74514073..74516992,2	MCF-7	breast:
2	chr15:74495538..74499115-chr15:74503082..74506667,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC33-1	chr15:74504823-74505314	ENSG00000259264.1

No data

Variant related genes	Relation type
STRA6	TF binding region
ENSG00000259264	TF binding region
CCDC33	TF binding region
ENSG00000137868	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1484211	1.00[EUR][1000 genomes]
rs240047	1.00[EUR][1000 genomes]
rs2629734	1.00[EUR][1000 genomes]
rs2930293	1.00[EUR][1000 genomes]
rs2930309	1.00[EUR][1000 genomes]
rs351163	1.00[EUR][1000 genomes]
rs351165	1.00[EUR][1000 genomes]
rs351167	1.00[EUR][1000 genomes]
rs351169	1.00[EUR][1000 genomes]
rs351183	1.00[EUR][1000 genomes]
rs351185	1.00[EUR][1000 genomes]
rs381832	1.00[EUR][1000 genomes]
rs440793	1.00[EUR][1000 genomes]
rs7171215	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936728	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833053	chr15:74360156-74555140	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv904345	chr15:74458181-74526596	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv904346	chr15:74458181-74548773	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv904347	chr15:74462629-74537101	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv904348	chr15:74462629-74542686	Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv471253	chr15:74489207-74545148	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv904349	chr15:74500105-74542686	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv904350	chr15:74500105-74548773	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74489200-74509600	Weak transcription	Gastric	stomach
2	chr15:74497000-74505800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:74498400-74506000	Weak transcription	Left Ventricle	heart
4	chr15:74500200-74506000	Weak transcription	Brain Germinal Matrix	brain
5	chr15:74500600-74506000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:74501200-74507400	Weak transcription	Spleen	Spleen
7	chr15:74501800-74505800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr15:74501800-74507200	Weak transcription	HSMM	muscle
9	chr15:74502000-74506000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:74502200-74506200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:74502200-74508800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:74502400-74507400	Weak transcription	Placenta	Placenta
13	chr15:74503000-74505800	Weak transcription	Fetal Lung	lung
14	chr15:74503000-74506000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr15:74503000-74506600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:74503000-74507000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:74503000-74507200	Weak transcription	Fetal Kidney	kidney
18	chr15:74503200-74505600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr15:74503200-74506000	Weak transcription	Fetal Stomach	stomach
20	chr15:74503200-74506200	Weak transcription	Right Atrium	heart
21	chr15:74503200-74507000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr15:74503200-74507000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr15:74503400-74506000	Weak transcription	Fetal Brain Female	brain
24	chr15:74503400-74506400	Weak transcription	NH-A	brain
25	chr15:74503600-74506000	Weak transcription	Fetal Heart	heart
26	chr15:74503600-74506200	Weak transcription	Osteobl	bone
27	chr15:74503800-74505600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr15:74503800-74505600	Weak transcription	Fetal Brain Male	brain
29	chr15:74503800-74507400	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr15:74504000-74508800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:74504000-74508800	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr15:74504200-74505000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr15:74504200-74506000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr15:74504200-74507000	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr15:74504200-74507200	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr15:74504200-74508200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr15:74504200-74508600	Enhancers	HepG2	liver
38	chr15:74504200-74508800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr15:74504200-74508800	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr15:74504400-74505200	Enhancers	Fetal Muscle Trunk	muscle
41	chr15:74504400-74505200	Flanking Active TSS	GM12878-XiMat	blood
42	chr15:74504400-74505800	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr15:74504400-74506800	Weak transcription	Hela-S3	cervix
44	chr15:74504400-74508400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:74504400-74508800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:74504400-74508800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:74504400-74508800	Enhancers	Fetal Thymus	thymus
48	chr15:74504400-74510400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr15:74504600-74505200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:74504600-74506000	Weak transcription	Lung	lung

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