Variant report

Variant	rs3759793
Chromosome Location	chr15:41806726-41806727
allele	A/C
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	JUN	chr15:41805585-41806855	K562	blood:	n/a	chr15:41806353-41806361 chr15:41806837-41806846
2	CUX1	chr15:41806439-41806784	K562	blood:	n/a	chr15:41806648-41806657 chr15:41806648-41806657

Variant related genes	Relation type
LTK	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1077809	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10851405	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11070331	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070332	0.81[AMR][1000 genomes]
rs1200340	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1200345	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs1200348	0.85[CHB][hapmap];0.93[CHD][hapmap]
rs1200349	0.85[CHB][hapmap];0.93[CHD][hapmap]
rs1867419	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2253936	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2274858	0.85[CHB][hapmap];0.88[CHD][hapmap]
rs2289739	0.87[GIH][hapmap]
rs2289740	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2297377	0.89[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs2297378	0.85[CHB][hapmap]
rs2777490	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs316622	0.89[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs316623	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8035331	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8035575	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv904110	chr15:41776692-41813279	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv471241	chr15:41783814-41820200	Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv904112	chr15:41806658-41836234	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3759793	NDUFAF1	cis	parietal	SCAN
rs3759793	RPAP1	cis	lymphoblastoid	GTEx
rs3759793	RPAP1	cis	parietal	SCAN
rs3759793	BUB1B	cis	parietal	SCAN
rs3759793	NDUFAF1	cis	lymphoblastoid	seeQTL
rs3759793	TYRO3	cis	parietal	SCAN
rs3759793	RPAP1	cis	lymphoblastoid	seeQTL
rs3759793	SPINT1	cis	parietal	SCAN
rs3759793	SPTBN5	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41801800-41819000	Weak transcription	Hela-S3	cervix
2	chr15:41805200-41809200	Weak transcription	A549	lung
3	chr15:41806000-41806800	Flanking Active TSS	K562	blood
4	chr15:41806000-41809400	Weak transcription	Brain Angular Gyrus	brain
5	chr15:41806200-41806800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:41806200-41806800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
7	chr15:41806200-41806800	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr15:41806200-41806800	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr15:41806200-41806800	Enhancers	Stomach Mucosa	stomach
10	chr15:41806200-41808600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr15:41806200-41809000	Weak transcription	Ovary	ovary
12	chr15:41806200-41809200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr15:41806200-41809200	Weak transcription	Left Ventricle	heart
14	chr15:41806200-41809600	Weak transcription	Colon Smooth Muscle	Colon
15	chr15:41806200-41809600	Weak transcription	Pancreas	Pancrea
16	chr15:41806200-41809600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr15:41806200-41809600	Weak transcription	HMEC	breast
18	chr15:41806200-41815400	Weak transcription	NHDF-Ad	bronchial
19	chr15:41806200-41820400	Weak transcription	HSMM	muscle
20	chr15:41806200-41822600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:41806400-41806800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr15:41806400-41806800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr15:41806400-41806800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr15:41806400-41806800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:41806400-41806800	Strong transcription	Brain Substantia Nigra	brain
26	chr15:41806400-41807200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr15:41806400-41808200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:41806400-41808600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:41806400-41808600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:41806400-41808800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:41806400-41808800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr15:41806400-41808800	Weak transcription	Fetal Intestine Small	intestine
33	chr15:41806400-41809000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr15:41806400-41809000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr15:41806400-41809000	Weak transcription	Placenta	Placenta
36	chr15:41806400-41809000	Weak transcription	NHEK	skin
37	chr15:41806400-41809200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:41806400-41809200	Weak transcription	NHLF	lung
39	chr15:41806400-41809400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr15:41806400-41809400	Weak transcription	Adipose Nuclei	Adipose
41	chr15:41806400-41809400	Weak transcription	Brain Anterior Caudate	brain
42	chr15:41806400-41809400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr15:41806400-41809400	Weak transcription	Fetal Intestine Large	intestine
44	chr15:41806400-41809400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr15:41806400-41809400	Weak transcription	Psoas Muscle	Psoas
46	chr15:41806400-41809400	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr15:41806400-41809400	Weak transcription	HSMMtube	muscle
48	chr15:41806400-41809600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:41806400-41809600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr15:41806400-41809600	Weak transcription	Esophagus	oesophagus

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