Variant report

Variant	rs28514579
Chromosome Location	chr19:36546956-36546957
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr19:36546937-36547435	MCF-7	breast:	n/a	n/a
2	HA-E2F1	chr19:36546646-36547377	MCF-7	breast:	n/a	n/a
3	MXI1	chr19:36543834-36547376	SK-N-SH	brain:	n/a	n/a
4	MAX	chr19:36546822-36547516	K562	blood:	n/a	chr19:36547261-36547271

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:36370756..36373249-chr19:36545654..36547165,2	MCF-7	breast:
2	chr19:36497884..36507784-chr19:36542079..36547610,17	MCF-7	breast:
3	chr19:36393181..36395162-chr19:36544398..36547293,2	K562	blood:
4	chr19:36484913..36488286-chr19:36544915..36548972,3	MCF-7	breast:
5	chr19:36484527..36490376-chr19:36543488..36547183,11	K562	blood:
6	chr19:36543278..36547003-chr19:36629856..36633093,3	MCF-7	breast:
7	chr19:36543835..36550918-chr19:36603651..36608049,11	MCF-7	breast:
8	chr19:36544655..36547364-chr19:36630776..36632492,2	K562	blood:
9	chr19:36504655..36506922-chr19:36544255..36547222,4	K562	blood:
10	chr19:36545240..36547330-chr19:36604696..36606743,2	K562	blood:
11	chr19:36496294..36501686-chr19:36543356..36547257,9	MCF-7	breast:
12	chr19:36543772..36546988-chr19:36561665..36565427,3	MCF-7	breast:

No data

Variant related genes	Relation type
THAP8	TF binding region
ENSG00000126264	Chromatin interaction
ENSG00000105258	Chromatin interaction
ENSG00000105254	Chromatin interaction
ENSG00000181392	Chromatin interaction
ENSG00000267698	Chromatin interaction
ENSG00000167604	Chromatin interaction
ENSG00000105261	Chromatin interaction
ENSG00000243968	Chromatin interaction
ENSG00000205138	Chromatin interaction
ENSG00000075702	Chromatin interaction
ENSG00000126247	Chromatin interaction
ENSG00000239382	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs13344701	0.85[ASN][1000 genomes]
rs13344825	0.85[ASN][1000 genomes]
rs17777328	0.82[ASN][1000 genomes]
rs35759606	0.82[ASN][1000 genomes]
rs9989683	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28514579	WDR62	cis	Nerve Tibial	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36543600-36547000	Active TSS	NHDF-Ad	bronchial
2	chr19:36544200-36547600	Active TSS	NHLF	lung
3	chr19:36544400-36547000	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr19:36544400-36547000	Active TSS	NH-A	brain
5	chr19:36544400-36547200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr19:36544400-36547200	Active TSS	H9 Cell Line	embryonic stem cell
7	chr19:36544400-36547200	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr19:36544400-36547200	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr19:36544400-36547400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:36544600-36547000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:36544600-36547200	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr19:36544600-36547200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr19:36544600-36547600	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr19:36544800-36547200	Active TSS	NHEK	skin
15	chr19:36545000-36547400	Active TSS	H1 Cell Line	embryonic stem cell
16	chr19:36545400-36547000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr19:36546000-36547000	Flanking Active TSS	Fetal Muscle Leg	muscle
18	chr19:36546200-36547000	Flanking Active TSS	Fetal Thymus	thymus
19	chr19:36546200-36547200	Flanking Active TSS	Thymus	Thymus
20	chr19:36546200-36547400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr19:36546200-36547400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr19:36546200-36547800	Flanking Active TSS	Brain Germinal Matrix	brain
23	chr19:36546400-36547000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:36546400-36547000	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr19:36546400-36547200	Flanking Active TSS	Dnd41	blood
26	chr19:36546400-36547800	Enhancers	Stomach Mucosa	stomach
27	chr19:36546400-36549600	Weak transcription	Gastric	stomach
28	chr19:36546400-36577600	Weak transcription	Esophagus	oesophagus
29	chr19:36546400-36584000	Weak transcription	Right Atrium	heart
30	chr19:36546600-36547000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:36546600-36547000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr19:36546600-36547000	Enhancers	Primary T cells fromperipheralblood	blood
33	chr19:36546600-36547000	Enhancers	Fetal Brain Male	brain
34	chr19:36546600-36547000	Flanking Active TSS	HepG2	liver
35	chr19:36546600-36547200	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr19:36546600-36547200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:36546600-36547200	Enhancers	Placenta	Placenta
38	chr19:36546600-36547400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr19:36546600-36547400	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr19:36546600-36547400	Active TSS	Fetal Brain Female	brain
41	chr19:36546600-36547600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr19:36546600-36547600	Enhancers	Fetal Lung	lung
43	chr19:36546600-36547600	Transcr. at gene 5' and 3'	A549	lung
44	chr19:36546600-36548000	Enhancers	Fetal Muscle Trunk	muscle
45	chr19:36546600-36549200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr19:36546600-36549400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:36546600-36549400	Weak transcription	Liver	Liver
48	chr19:36546600-36549400	Weak transcription	Psoas Muscle	Psoas
49	chr19:36546600-36549400	Weak transcription	HSMMtube	muscle
50	chr19:36546600-36551000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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