Variant report

Variant	rs28570610
Chromosome Location	chr15:83731787-83731788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:45)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:45 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF4	chr15:83731481-83732023	GM12878	blood:	n/a	n/a
2	BATF	chr15:83731621-83731923	GM12878	blood:	n/a	n/a
3	ATF1	chr15:83731414-83731876	K562	blood:	n/a	n/a
4	JUND	chr15:83731402-83731816	K562	blood:	n/a	n/a
5	SPI1	chr15:83731496-83731920	K562	blood:	n/a	n/a
6	IRF1	chr15:83731547-83731871	K562	blood:	n/a	n/a
7	EP300	chr15:83731629-83731994	GM12878	blood:	n/a	n/a
8	NFATC1	chr15:83731439-83732037	GM12878	blood:	n/a	n/a
9	CHD1	chr15:83731562-83732143	GM12878	blood:	n/a	n/a
10	BHLHE40	chr15:83731412-83731976	GM12878	blood:	n/a	n/a
11	POLR2A	chr15:83731135-83732975	K562	blood:	n/a	n/a
12	SPI1	chr15:83731407-83731999	GM12878	blood:	n/a	n/a
13	CUX1	chr15:83731525-83732164	K562	blood:	n/a	n/a
14	TEAD4	chr15:83731423-83732132	K562	blood:	n/a	n/a
15	CHD2	chr15:83731522-83731991	GM12878	blood:	n/a	n/a
16	RCOR1	chr15:83731457-83731819	K562	blood:	n/a	n/a
17	CUX1	chr15:83731364-83732037	GM12878	blood:	n/a	n/a
18	UBTF	chr15:83731589-83731876	K562	blood:	n/a	n/a
19	IRF4	chr15:83731407-83732101	GM12878	blood:	n/a	n/a
20	EBF1	chr15:83731432-83731799	GM12878	blood:	n/a	n/a
21	MYC	chr15:83731457-83731800	K562	blood:	n/a	n/a
22	EP300	chr15:83731590-83732112	GM12878	blood:	n/a	n/a
23	SPI1	chr15:83731118-83732271	GM12878	blood:	n/a	n/a
24	STAT3	chr15:83731398-83732240	GM12878	blood:	n/a	chr15:83731526-83731538
25	SPI1	chr15:83731429-83732079	GM12891	blood:	n/a	n/a
26	SPI1	chr15:83731548-83731985	GM12878	blood:	n/a	n/a
27	JUN	chr15:83731489-83731907	K562	blood:	n/a	n/a
28	TBL1XR1	chr15:83731299-83732065	GM12878	blood:	n/a	n/a
29	TBP	chr15:83731622-83732096	GM12878	blood:	n/a	n/a
30	BCL11A	chr15:83731438-83731969	GM12878	blood:	n/a	n/a
31	MXI1	chr15:83731439-83732107	GM12878	blood:	n/a	n/a
32	EP300	chr15:83731426-83732130	GM12878	blood:	n/a	n/a
33	NFIC	chr15:83731368-83732064	GM12878	blood:	n/a	n/a
34	REST	chr15:83731600-83731908	Hela-S3	cervix:	n/a	n/a
35	SPI1	chr15:83731455-83732029	HL-60	blood:	n/a	n/a
36	MTA3	chr15:83731336-83732322	GM12878	blood:	n/a	n/a
37	ATF2	chr15:83731346-83732189	GM12878	blood:	n/a	n/a
38	IKZF1	chr15:83731322-83732324	GM12878	blood:	n/a	n/a
39	TAL1	chr15:83731537-83731866	K562	blood:	n/a	n/a
40	RUNX3	chr15:83731472-83732039	GM12878	blood:	n/a	n/a
41	RUNX3	chr15:83731561-83731972	GM12878	blood:	n/a	n/a
42	SPI1	chr15:83731376-83732058	GM12891	blood:	n/a	n/a
43	BATF	chr15:83731651-83732046	GM12878	blood:	n/a	n/a
44	SPI1	chr15:83731406-83732105	HL-60	blood:	n/a	n/a
45	BCLAF1	chr15:83731413-83732060	GM12878	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:83731597..83733355-chr15:83864514..83866246,2	K562	blood:
2	chr15:83731060..83733792-chr15:83908261..83911046,2	K562	blood:
3	chr15:83678535..83684480-chr15:83731660..83738533,12	MCF-7	breast:
4	chr15:83684703..83687598-chr15:83730655..83733296,2	K562	blood:
5	chr15:83731075..83738271-chr15:83771545..83781798,12	K562	blood:
6	chr15:83728223..83733279-chr15:83872338..83876797,5	MCF-7	breast:
7	chr15:83730196..83733187-chr15:83768723..83771408,2	K562	blood:
8	chr15:83684589..83686265-chr15:83730370..83733896,3	K562	blood:
9	chr15:83729958..83731918-chr15:83873754..83876492,2	K562	blood:

No data

Variant related genes	Relation type
MIR4515	TF binding region
ENSG00000136404	Chromatin interaction
ENSG00000166503	Chromatin interaction
ENSG00000260608	Chromatin interaction
ENSG00000169609	Chromatin interaction
ENSG00000249214	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10220725	1.00[ASN][1000 genomes]
rs17295457	1.00[ASN][1000 genomes]
rs28408839	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28429062	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28454771	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28463621	1.00[ASN][1000 genomes]
rs28479338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28509292	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28510490	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28540116	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28569354	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28662361	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28707195	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28711332	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28755408	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28819476	1.00[ASN][1000 genomes]
rs28836869	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67634629	1.00[ASN][1000 genomes]
rs7169539	1.00[ASN][1000 genomes]
rs7170046	1.00[ASN][1000 genomes]
rs72755930	1.00[ASN][1000 genomes]
rs72755935	1.00[ASN][1000 genomes]
rs72755947	1.00[ASN][1000 genomes]
rs72755962	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025896	0.84[AFR][1000 genomes]
rs8038619	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9919979	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040336	chr15:83578947-83768335	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv482308	chr15:83584918-83747362	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28570610	HDGFRP3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83681600-83732000	Weak transcription	Stomach Mucosa	stomach
2	chr15:83700400-83734400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:83701600-83732800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:83722600-83732800	Weak transcription	NHLF	lung
5	chr15:83725000-83733800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:83725200-83732200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr15:83725200-83732200	Weak transcription	Thymus	Thymus
8	chr15:83725200-83732400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:83725400-83734600	Weak transcription	Placenta	Placenta
10	chr15:83725600-83734400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:83726800-83732400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:83726800-83733600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:83727000-83731800	Weak transcription	Fetal Stomach	stomach
14	chr15:83727000-83732000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr15:83727000-83732200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr15:83727000-83732200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr15:83727200-83732400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr15:83727400-83732200	Weak transcription	Aorta	Aorta
19	chr15:83727400-83734200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr15:83727800-83732200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr15:83729400-83733200	Enhancers	Fetal Intestine Large	intestine
22	chr15:83729600-83732600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:83729600-83733000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr15:83729600-83733800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr15:83729600-83733800	Enhancers	Fetal Kidney	kidney
26	chr15:83729800-83731800	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:83729800-83731800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:83729800-83732000	Genic enhancers	Hela-S3	cervix
29	chr15:83729800-83732400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr15:83729800-83732800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:83729800-83732800	Enhancers	Colon Smooth Muscle	Colon
32	chr15:83729800-83733600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr15:83729800-83733600	Enhancers	Fetal Heart	heart
34	chr15:83729800-83733800	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr15:83729800-83734400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr15:83730000-83732200	Enhancers	Brain Cingulate Gyrus	brain
37	chr15:83730000-83732400	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr15:83730000-83732800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:83730000-83733400	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr15:83730200-83732000	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr15:83730200-83732200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr15:83730200-83732200	Enhancers	Muscle Satellite Cultured Cells	--
43	chr15:83730200-83732400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr15:83730200-83732600	Genic enhancers	HepG2	liver
45	chr15:83730200-83732600	Genic enhancers	NHEK	skin
46	chr15:83730200-83733000	Enhancers	Osteobl	bone
47	chr15:83730200-83733200	Enhancers	NH-A	brain
48	chr15:83730200-83733400	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr15:83730200-83733600	Enhancers	NHDF-Ad	bronchial
50	chr15:83730200-83734600	Enhancers	Small Intestine	intestine

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