Variant report

Variant	rs28418513
Chromosome Location	chr15:59950332-59950333
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:59949098-59950454	HepG2	liver:	n/a	n/a
2	MXI1	chr15:59948690-59950336	SK-N-SH	brain:	n/a	n/a
3	CBX3	chr15:59949520-59950387	K562	blood:	n/a	n/a
4	POLR2A	chr15:59950242-59950346	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr15:59949456-59950789	K562	blood:	n/a	n/a
6	SETDB1	chr15:59949845-59950499	U2OS	brain:	n/a	n/a
7	HCFC1	chr15:59948592-59950339	Hela-S3	cervix:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:59680945..59682711-chr15:59948219..59950781,2	MCF-7	breast:
2	chr15:59948214..59950768-chr15:59963899..59966386,2	K562	blood:
3	chr15:59949368..59951651-chr15:60769964..60772749,2	K562	blood:
4	chr15:59947605..59950537-chr15:59979625..59981765,3	MCF-7	breast:
5	chr15:59945879..59953077-chr15:59978622..59984049,13	K562	blood:
6	chr15:59949843..59951651-chr15:60768775..60771464,2	K562	blood:
7	chr15:59946363..59951356-chr15:59979923..59984049,7	K562	blood:

No data

Variant related genes	Relation type
GTF2A2	TF binding region
ENSG00000140299	Chromatin interaction
ENSG00000259238	Chromatin interaction
ENSG00000238767	Chromatin interaction
ENSG00000227161	Chromatin interaction
ENSG00000245534	Chromatin interaction
ENSG00000128915	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12050786	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs16941544	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17236713	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17236734	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17302448	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17302608	0.85[EUR][1000 genomes]
rs28395445	0.95[EUR][1000 genomes]
rs28422085	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28437066	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28642859	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28654927	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28883924	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4775192	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4775193	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4775198	0.95[EUR][1000 genomes]
rs6151457	0.85[EUR][1000 genomes]
rs6151492	0.85[EUR][1000 genomes]
rs6151497	0.85[EUR][1000 genomes]
rs6151505	0.85[EUR][1000 genomes]
rs6151522	0.95[EUR][1000 genomes]
rs6151534	0.95[EUR][1000 genomes]
rs6151538	0.95[EUR][1000 genomes]
rs6151540	0.95[EUR][1000 genomes]
rs6151567	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6151575	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6151591	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7178008	0.84[EUR][1000 genomes]
rs8027421	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8033208	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8033718	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1044442	chr15:59765724-59955587	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv542403	chr15:59765724-59955587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv569605	chr15:59855226-59956553	Strong transcription Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv533240	chr15:59858093-59998176	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1824522	chr15:59919844-59987181	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv1043693	chr15:59944471-59971500	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59947600-59950400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr15:59948400-59950400	Active TSS	Right Atrium	heart
3	chr15:59948600-59950400	Active TSS	Fetal Intestine Large	intestine
4	chr15:59948600-59950400	Active TSS	Psoas Muscle	Psoas
5	chr15:59948600-59950600	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr15:59948800-59950400	Active TSS	Brain Anterior Caudate	brain
7	chr15:59948800-59950400	Active TSS	Brain Germinal Matrix	brain
8	chr15:59948800-59950400	Active TSS	Brain Hippocampus Middle	brain
9	chr15:59949000-59950400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:59949000-59950400	Active TSS	Brain Cingulate Gyrus	brain
11	chr15:59949000-59950400	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr15:59949000-59950400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:59949000-59950400	Active TSS	Brain Substantia Nigra	brain
14	chr15:59949000-59950400	Active TSS	Duodenum Mucosa	Duodenum
15	chr15:59949000-59950400	Active TSS	Fetal Lung	lung
16	chr15:59949000-59950400	Active TSS	Rectal Smooth Muscle	rectum
17	chr15:59949000-59950400	Active TSS	Stomach Smooth Muscle	stomach
18	chr15:59949000-59950800	Active TSS	Placenta	Placenta
19	chr15:59949200-59950400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:59949200-59950400	Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr15:59949400-59950400	Active TSS	Adipose Nuclei	Adipose
22	chr15:59949400-59960200	Weak transcription	Fetal Heart	heart
23	chr15:59949600-59950400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr15:59949800-59950400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr15:59949800-59950400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr15:59949800-59951400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr15:59949800-59954600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr15:59949800-59954600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:59949800-59957200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr15:59949800-59957200	Weak transcription	Spleen	Spleen
31	chr15:59949800-59963400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr15:59949800-59964000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr15:59949800-59968000	Weak transcription	Stomach Mucosa	stomach
34	chr15:59949800-59968400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:59949800-59980000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr15:59950000-59950400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
37	chr15:59950000-59950400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr15:59950000-59950400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr15:59950000-59950400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr15:59950000-59950400	Flanking Active TSS	Dnd41	blood
41	chr15:59950000-59950600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr15:59950000-59963200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr15:59950200-59950400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:59950200-59950400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:59950200-59950400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr15:59950200-59950400	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr15:59950200-59950400	Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr15:59950200-59950400	Enhancers	Primary B cells from cord blood	blood
49	chr15:59950200-59950400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr15:59950200-59950400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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