Variant report

Variant	rs28711332
Chromosome Location	chr15:83728710-83728711
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:83728697-83728832	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:83679454..83682209-chr15:83728232..83730489,3	K562	blood:
2	chr15:83718422..83721272-chr15:83727802..83729791,2	MCF-7	breast:
3	chr15:83726826..83729671-chr15:83873975..83877192,5	MCF-7	breast:
4	chr15:83723627..83726592-chr15:83727241..83728963,2	MCF-7	breast:
5	chr15:83728223..83733279-chr15:83872338..83876797,5	MCF-7	breast:

No data

Variant related genes	Relation type
BTBD1	TF binding region
ENSG00000260608	Chromatin interaction
ENSG00000166503	Chromatin interaction
ENSG00000169609	Chromatin interaction
ENSG00000064726	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10220725	1.00[ASN][1000 genomes]
rs11857990	1.00[CHD][hapmap]
rs17295457	1.00[CHD][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs28408839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28429062	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28454771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28463621	1.00[ASN][1000 genomes]
rs28479338	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28509292	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28510490	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28540116	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28569354	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28570610	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28662361	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28707195	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28755408	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28819476	1.00[ASN][1000 genomes]
rs28836869	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67634629	1.00[ASN][1000 genomes]
rs716886	1.00[CHD][hapmap]
rs7169539	1.00[ASN][1000 genomes]
rs7170046	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7173876	1.00[CEU][hapmap]
rs7177462	1.00[CHD][hapmap]
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	0.81[AFR][1000 genomes]
rs8038619	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9919979	1.00[CEU][hapmap];0.82[YRI][hapmap];0.93[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
rs28711332	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	chr15:83705000-83731000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr15:83709600-83730800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr15:83710600-83730200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:83710600-83730200	Weak transcription	Esophagus	oesophagus
8	chr15:83714200-83730200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:83717400-83731400	Weak transcription	Spleen	Spleen
10	chr15:83718000-83731000	Weak transcription	Colonic Mucosa	Colon
11	chr15:83719800-83729800	Weak transcription	NHEK	skin
12	chr15:83720000-83729800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:83722400-83730200	Weak transcription	HSMMtube	muscle
14	chr15:83722600-83730200	Weak transcription	NHDF-Ad	bronchial
15	chr15:83722600-83732800	Weak transcription	NHLF	lung
16	chr15:83722800-83730200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr15:83723400-83729600	Weak transcription	Fetal Kidney	kidney
18	chr15:83723800-83729800	Weak transcription	HMEC	breast
19	chr15:83724800-83729800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr15:83724800-83729800	Weak transcription	A549	lung
21	chr15:83724800-83729800	Weak transcription	Hela-S3	cervix
22	chr15:83724800-83730200	Weak transcription	Lung	lung
23	chr15:83724800-83730600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr15:83724800-83730600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr15:83724800-83731000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:83724800-83731400	Weak transcription	Brain Germinal Matrix	brain
27	chr15:83725000-83729800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr15:83725000-83733800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr15:83725200-83730000	Weak transcription	HUVEC	blood vessel
30	chr15:83725200-83730200	Weak transcription	NH-A	brain
31	chr15:83725200-83730200	Weak transcription	Osteobl	bone
32	chr15:83725200-83732200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr15:83725200-83732200	Weak transcription	Thymus	Thymus
34	chr15:83725200-83732400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:83725400-83729800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr15:83725400-83729800	Weak transcription	Liver	Liver
37	chr15:83725400-83730400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr15:83725400-83730600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:83725400-83730600	Weak transcription	Adipose Nuclei	Adipose
40	chr15:83725400-83731200	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr15:83725400-83734600	Weak transcription	Placenta	Placenta
42	chr15:83725600-83734400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr15:83725800-83729600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr15:83726000-83729800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr15:83726000-83729800	Weak transcription	Brain Substantia Nigra	brain
46	chr15:83726000-83729800	Weak transcription	HSMM	muscle
47	chr15:83726000-83730000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr15:83726000-83730400	Weak transcription	Fetal Thymus	thymus
49	chr15:83726000-83730400	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr15:83726000-83731000	Weak transcription	Primary monocytes fromperipheralblood	blood

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