Variant report

Variant	rs3743033
Chromosome Location	chr15:41101124-41101125
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr15:41101108-41101387	GM12878	blood:	n/a	n/a
2	SREBP1	chr15:41098583-41101657	GM12878	blood:	n/a	n/a
3	RUNX3	chr15:41101113-41101528	GM12878	blood:	n/a	n/a
4	EBF1	chr15:41101112-41101334	GM12878	blood:	n/a	n/a
5	HCFC1	chr15:41098689-41102091	Hela-S3	cervix:	n/a	n/a
6	TCF12	chr15:41101112-41101342	GM12878	blood:	n/a	n/a
7	STAT3	chr15:41101109-41101326	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41045748..41048901-chr15:41096709..41101394,9	K562	blood:
2	chr15:41099271..41102222-chr15:41135281..41137187,2	K562	blood:
3	chr15:41098123..41102222-chr15:41134582..41138137,4	K562	blood:
4	chr15:41095442..41103026-chr15:41134658..41140625,11	MCF-7	breast:
5	chr15:41097893..41103310-chr15:41103796..41109268,7	MCF-7	breast:
6	chr15:41100855..41102435-chr15:41184867..41186640,2	K562	blood:
7	chr15:41098435..41103357-chr15:41133527..41139132,10	MCF-7	breast:
8	chr15:41045813..41047463-chr15:41099042..41101691,3	K562	blood:

No data

Variant related genes	Relation type
ZFYVE19	TF binding region
DNAJC17	TF binding region
ENSG00000166145	Chromatin interaction
ENSG00000104142	Chromatin interaction
ENSG00000137824	Chromatin interaction
ENSG00000166140	Chromatin interaction
ENSG00000261183	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10152371	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11070294	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11070295	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11070296	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11070297	0.88[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11856866	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858010	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12148058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12899910	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12905621	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12909824	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12916485	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12916535	0.85[EUR][1000 genomes]
rs17657877	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17657986	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2010300	0.84[CEU][hapmap];0.81[MEX][hapmap]
rs2289219	0.84[CEU][hapmap]
rs2412567	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs2899000	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs34143869	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34817886	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34948298	0.90[EUR][1000 genomes]
rs35458726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35621205	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35853942	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3736286	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3743034	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4402538	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56886112	0.88[EUR][1000 genomes]
rs57818172	0.88[EUR][1000 genomes]
rs57825040	0.88[EUR][1000 genomes]
rs57943888	0.88[EUR][1000 genomes]
rs57994257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62018584	0.81[EUR][1000 genomes]
rs62018585	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6492967	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs745032	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8036842	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8037830	0.88[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[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	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs3743033	MRPL42P5	cis	multi-tissue	Pritchard
rs3743033	ZFYVE19	cis	Nerve Tibial	GTEx
rs3743033	ZFYVE19	cis	multi-tissue	Pritchard
rs3743033	ZFYVE19	cis	Artery Aorta	GTEx
rs3743033	RP11-111A22.1	cis	Artery Tibial	GTEx
rs3743033	ZFYVE19	cis	Thyroid	GTEx
rs3743033	PLCB2	cis	multi-tissue	Pritchard
rs3743033	ZFYVE19	cis	Artery Tibial	GTEx
rs3743033	C15orf57	cis	Artery Tibial	GTEx
rs3743033	C15orf57	cis	Adipose Subcutaneous	GTEx
rs3743033	CCDC32	cis	multi-tissue	Pritchard
rs3743033	ZFYVE19	cis	Esophagus Muscularis	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41100000-41101200	Flanking Active TSS	Dnd41	blood
2	chr15:41100000-41101400	Flanking Active TSS	Duodenum Mucosa	Duodenum
3	chr15:41100200-41101200	Flanking Active TSS	Hela-S3	cervix
4	chr15:41100200-41101400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:41100200-41107600	Weak transcription	Aorta	Aorta
6	chr15:41100400-41101200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr15:41100400-41101200	Enhancers	Fetal Intestine Large	intestine
8	chr15:41100400-41101200	Enhancers	Fetal Intestine Small	intestine
9	chr15:41100400-41101400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:41100400-41101400	Enhancers	Lung	lung
11	chr15:41100400-41101400	Enhancers	Placenta Amnion	Placenta Amnion
12	chr15:41100400-41101600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr15:41100400-41101800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:41100400-41101800	Weak transcription	Ovary	ovary
15	chr15:41100400-41101800	Flanking Active TSS	GM12878-XiMat	blood
16	chr15:41100400-41102400	Weak transcription	Left Ventricle	heart
17	chr15:41100400-41107800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr15:41100600-41101200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr15:41100600-41101200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:41100600-41101200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr15:41100600-41101200	Enhancers	Fetal Muscle Leg	muscle
22	chr15:41100600-41101400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:41100600-41101400	Enhancers	Primary T cells fromperipheralblood	blood
24	chr15:41100600-41101400	Weak transcription	Esophagus	oesophagus
25	chr15:41100600-41101400	Enhancers	Fetal Muscle Trunk	muscle
26	chr15:41100600-41101600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:41100600-41101600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr15:41100600-41101600	Enhancers	Fetal Lung	lung
29	chr15:41100600-41101600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr15:41100600-41101800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr15:41100600-41101800	Weak transcription	Fetal Stomach	stomach
32	chr15:41100600-41101800	Enhancers	Fetal Thymus	thymus
33	chr15:41100600-41102200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr15:41100600-41102200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr15:41100600-41102200	Weak transcription	Right Ventricle	heart
36	chr15:41100600-41102600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr15:41100600-41102600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr15:41100600-41102800	Weak transcription	HSMMtube	muscle
39	chr15:41100600-41103000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr15:41100600-41103000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:41100600-41103400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr15:41100600-41103800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr15:41100600-41104600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr15:41100600-41107800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr15:41100600-41108800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:41100600-41108800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr15:41100800-41101200	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr15:41100800-41101200	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr15:41100800-41101200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr15:41100800-41101200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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