Variant report

Variant	rs6766038
Chromosome Location	chr3:52446788-52446789
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	CTCF	chr3:52446680-52446830	HFF	foreskin:	n/a	n/a
2	REST	chr3:52446755-52447380	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52444067..52446922-chr3:52566590..52568238,2	K562	blood:
2	chr3:52445308..52446845-chr3:52482628..52484238,2	MCF-7	breast:
3	chr3:52445710..52451315-chr3:52451741..52455746,7	K562	blood:

Variant related genes	Relation type
BAP1	TF binding region
PHF7	TF binding region
ENSG00000168273	Chromatin interaction
ENSG00000010318	Chromatin interaction
ENSG00000168268	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs17052326	1.00[EUR][1000 genomes]
rs2577828	1.00[EUR][1000 genomes]
rs2577829	1.00[EUR][1000 genomes]
rs2577830	1.00[EUR][1000 genomes]
rs2590841	1.00[EUR][1000 genomes]
rs3844291	0.83[YRI][hapmap]
rs3890123	0.82[ASW][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs4234635	1.00[EUR][1000 genomes]
rs4234636	1.00[EUR][1000 genomes]
rs55971019	1.00[AMR][1000 genomes]
rs56866386	1.00[EUR][1000 genomes]
rs56898787	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56961704	1.00[AMR][1000 genomes]
rs58781613	1.00[AMR][1000 genomes]
rs60499166	1.00[AMR][1000 genomes]
rs60997031	1.00[AMR][1000 genomes]
rs61734628	1.00[AMR][1000 genomes]
rs72947525	1.00[EUR][1000 genomes]
rs72947530	1.00[EUR][1000 genomes]
rs72947531	1.00[EUR][1000 genomes]
rs72947532	1.00[EUR][1000 genomes]
rs72947537	1.00[EUR][1000 genomes]
rs72947557	1.00[EUR][1000 genomes]
rs72959348	1.00[EUR][1000 genomes]
rs72965274	1.00[EUR][1000 genomes]
rs73835766	1.00[AMR][1000 genomes]
rs73837049	1.00[AMR][1000 genomes]
rs73837599	1.00[AMR][1000 genomes]
rs73838354	1.00[AMR][1000 genomes]
rs73839116	1.00[AMR][1000 genomes]
rs73839117	1.00[AMR][1000 genomes]
rs7614535	1.00[TSI][hapmap]
rs7638914	1.00[AMR][1000 genomes]
rs7641255	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
4	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6766038	NEK4	cis	lymphoblastoid	seeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52443400-52446800	Active TSS	Psoas Muscle	Psoas
2	chr3:52444800-52447000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:52445000-52446800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:52445000-52446800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:52445000-52446800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
6	chr3:52445000-52447000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:52445200-52446800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr3:52445200-52446800	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr3:52445200-52446800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
10	chr3:52445200-52446800	Flanking Active TSS	GM12878-XiMat	blood
11	chr3:52445400-52446800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:52445400-52446800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:52445400-52446800	Flanking Active TSS	NHEK	skin
14	chr3:52445600-52446800	Enhancers	Primary B cells from cord blood	blood
15	chr3:52445600-52446800	Enhancers	Primary B cells from peripheral blood	blood
16	chr3:52445600-52446800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:52445600-52446800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:52445600-52446800	Flanking Active TSS	Brain Anterior Caudate	brain
19	chr3:52445600-52446800	Flanking Active TSS	HMEC	breast
20	chr3:52445600-52447000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr3:52445600-52447200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:52445600-52447200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:52445600-52447200	Enhancers	Placenta Amnion	Placenta Amnion
24	chr3:52445600-52447200	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr3:52445600-52447200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr3:52445600-52447400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr3:52445600-52471600	Weak transcription	Gastric	stomach
28	chr3:52445800-52446800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:52445800-52446800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:52445800-52446800	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr3:52445800-52446800	Enhancers	HSMMtube	muscle
32	chr3:52445800-52447000	Enhancers	Primary T cells from cord blood	blood
33	chr3:52445800-52447000	Flanking Active TSS	NHDF-Ad	bronchial
34	chr3:52445800-52447200	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr3:52445800-52447200	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr3:52445800-52447400	Enhancers	Stomach Mucosa	stomach
37	chr3:52445800-52456800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr3:52445800-52457200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:52445800-52457600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr3:52446000-52446800	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr3:52446000-52446800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:52446000-52446800	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr3:52446000-52446800	Enhancers	Brain Substantia Nigra	brain
44	chr3:52446000-52446800	Enhancers	Fetal Brain Male	brain
45	chr3:52446000-52447000	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr3:52446000-52447000	Enhancers	Fetal Lung	lung
47	chr3:52446000-52447200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr3:52446000-52447400	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr3:52446000-52447600	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr3:52446000-52450400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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