Variant report

Variant	rs13326525
Chromosome Location	chr3:56650708-56650709
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:56650093-56650979	Hela-S3	cervix:	n/a	n/a
2	MAFK	chr3:56650162-56651062	GM12878	blood:	n/a	chr3:56650692-56650707
3	POLR2A	chr3:56650658-56651010	SK-N-MC	brain:	n/a	n/a
4	BACH1	chr3:56650516-56650965	K562	blood:	n/a	n/a
5	MAFK	chr3:56650525-56650954	HepG2	liver:	n/a	chr3:56650692-56650707
6	MAFK	chr3:56650509-56650888	K562	blood:	n/a	chr3:56650692-56650707
7	POLR2A	chr3:56650411-56650809	K562	blood:	n/a	n/a
8	MAFK	chr3:56650514-56650890	HepG2	liver:	n/a	chr3:56650692-56650707
9	MAFK	chr3:56650512-56650947	Hela-S3	cervix:	n/a	chr3:56650692-56650707
10	MAFF	chr3:56650512-56650906	HepG2	liver:	n/a	chr3:56650690-56650708
11	EP300	chr3:56650555-56650720	K562	blood:	n/a	n/a
12	POLR2A	chr3:56648967-56664047	K562	blood:	n/a	n/a
13	BACH1	chr3:56650518-56650959	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAFF	chr3:56650515-56650889	K562	blood:	n/a	chr3:56650690-56650708
15	MAFK	chr3:56650513-56650891	IMR90	lung:	n/a	chr3:56650692-56650707
16	MAFK	chr3:56650523-56650888	H1-hESC	embryonic stem cell:	n/a	chr3:56650692-56650707

Variant related genes	Relation type
CCDC66	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11130524	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs13316272	1.00[AMR][1000 genomes]
rs13320990	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28605592	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9817151	1.00[AMR][1000 genomes]
rs9821740	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9824415	1.00[AMR][1000 genomes]
rs9827937	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9846575	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9848723	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs9853548	0.82[YRI][hapmap];0.90[AFR][1000 genomes]
rs9861624	1.00[AMR][1000 genomes]
rs9864263	1.00[AMR][1000 genomes]
rs9867688	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9873327	0.94[AFR][1000 genomes]
rs9877962	0.85[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9883323	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9985426	1.00[AMR][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	nsv460557	chr3:56594735-56661320	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv590362	chr3:56594735-56661320	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13326525	HDGFRP3	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56625200-56653400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:56626400-56656200	Weak transcription	Stomach Mucosa	stomach
3	chr3:56630000-56654400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:56634000-56651400	Weak transcription	Fetal Brain Male	brain
5	chr3:56640400-56650800	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:56640600-56652600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:56640800-56650800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:56640800-56664200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:56640800-56695400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:56642800-56713400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:56644200-56664000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:56644400-56652000	Strong transcription	Fetal Lung	lung
13	chr3:56644400-56686400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:56644600-56655800	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:56644600-56665600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:56644600-56668600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:56644800-56655400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:56644800-56656000	Strong transcription	Fetal Muscle Leg	muscle
19	chr3:56644800-56669800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:56644800-56708200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr3:56645000-56650800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:56645200-56651600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:56645200-56657000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:56645400-56653800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:56645400-56667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:56645400-56705200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr3:56645600-56653400	Weak transcription	Fetal Heart	heart
28	chr3:56645600-56656000	Strong transcription	Fetal Intestine Large	intestine
29	chr3:56645600-56656000	Strong transcription	Fetal Muscle Trunk	muscle
30	chr3:56645600-56664800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:56645600-56665800	Strong transcription	Hela-S3	cervix
32	chr3:56645800-56662000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:56645800-56663800	Strong transcription	HSMM	muscle
34	chr3:56646000-56662800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:56646200-56659200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:56646600-56669000	Weak transcription	Small Intestine	intestine
37	chr3:56646800-56658800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:56646800-56659200	Weak transcription	Fetal Intestine Small	intestine
39	chr3:56646800-56673600	Weak transcription	Right Ventricle	heart
40	chr3:56647000-56658400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:56647000-56662000	Weak transcription	Esophagus	oesophagus
42	chr3:56647000-56663000	Strong transcription	Liver	Liver
43	chr3:56647000-56664000	Strong transcription	Adipose Nuclei	Adipose
44	chr3:56647000-56666800	Weak transcription	Lung	lung
45	chr3:56647000-56672200	Weak transcription	Gastric	stomach
46	chr3:56647200-56662600	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:56647200-56664000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr3:56647200-56664000	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr3:56647400-56655400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:56647400-56663800	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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