Variant report

Variant	rs3760487
Chromosome Location	chr17:19652575-19652576
allele	C/T
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	NFIC	chr17:19651425-19652701	ECC-1	luminal epithelium:	n/a	n/a
2	BCL3	chr17:19647775-19653407	A549	lung:	n/a	chr17:19652977-19652986 chr17:19650882-19650891 chr17:19650661-19650670 chr17:19652047-19652060
3	MAX	chr17:19651723-19652616	ECC-1	luminal epithelium:	n/a	chr17:19651879-19651888
4	CEBPB	chr17:19651285-19652664	A549	lung:	n/a	n/a
5	FOXA2	chr17:19650836-19652908	A549	lung:	n/a	n/a
6	REST	chr17:19649555-19652980	A549	lung:	n/a	chr17:19650573-19650591 chr17:19652049-19652062 chr17:19652019-19652029
7	TCF12	chr17:19647575-19653308	A549	lung:	n/a	chr17:19648161-19648171 chr17:19648468-19648475 chr17:19648978-19648985 chr17:19651904-19651912
8	MAX	chr17:19652162-19652639	ECC-1	luminal epithelium:	n/a	n/a
9	SIX5	chr17:19650107-19653086	A549	lung:	n/a	n/a
10	SP1	chr17:19648147-19652905	A549	lung:	n/a	chr17:19650262-19650269 chr17:19648213-19648225 chr17:19648215-19648224 chr17:19650286-19650300 chr17:19648214-19648223 chr17:19648209-19648223 chr17:19648214-19648224 chr17:19648492-19648506 chr17:19648223-19648233 chr17:19648213-19648225 chr17:19648214-19648228
11	TCF12	chr17:19651355-19652894	ECC-1	luminal epithelium:	n/a	chr17:19651904-19651912
12	E2F6	chr17:19650119-19653193	A549	lung:	n/a	chr17:19652359-19652371
13	CTCF	chr17:19647746-19653300	A549	lung:	n/a	chr17:19648889-19648902 chr17:19650591-19650599 chr17:19651387-19651397 chr17:19649367-19649376
14	EP300	chr17:19651449-19652603	ECC-1	luminal epithelium:	n/a	chr17:19651868-19651878 chr17:19651785-19651795
15	NFIC	chr17:19651516-19652664	ECC-1	luminal epithelium:	n/a	n/a
16	MAX	chr17:19648056-19653846	A549	lung:	n/a	chr17:19651879-19651888 chr17:19648221-19648230 chr17:19648968-19648984
17	SP1	chr17:19648113-19653000	A549	lung:	n/a	chr17:19652977-19652986 chr17:19650262-19650269 chr17:19648213-19648225 chr17:19648215-19648224 chr17:19650286-19650300 chr17:19652976-19652985 chr17:19648214-19648223 chr17:19648209-19648223 chr17:19652975-19652987 chr17:19648214-19648224 chr17:19648492-19648506 chr17:19648223-19648233 chr17:19648213-19648225 chr17:19648214-19648228
18	TCF12	chr17:19651421-19652649	ECC-1	luminal epithelium:	n/a	chr17:19651904-19651912
19	EP300	chr17:19651454-19652862	ECC-1	luminal epithelium:	n/a	chr17:19651868-19651878 chr17:19652732-19652741 chr17:19651785-19651795
20	SIN3AK20	chr17:19652121-19652634	A549	lung:	n/a	n/a
21	EP300	chr17:19649666-19653003	A549	lung:	n/a	chr17:19650306-19650322 chr17:19651055-19651065 chr17:19651868-19651878 chr17:19652732-19652741 chr17:19651785-19651795
22	FOXM1	chr17:19651455-19652690	ECC-1	luminal epithelium:	n/a	n/a
23	GATA3	chr17:19648106-19652992	A549	lung:	n/a	chr17:19650936-19650945 chr17:19649206-19649217
24	EP300	chr17:19649474-19652949	A549	lung:	n/a	chr17:19650306-19650322 chr17:19651055-19651065 chr17:19651868-19651878 chr17:19652732-19652741 chr17:19651785-19651795
25	MAX	chr17:19650448-19653274	A549	lung:	n/a	chr17:19651879-19651888
26	E2F6	chr17:19651750-19652647	A549	lung:	n/a	chr17:19652359-19652371

No.	Distal block	Cell Line	Cell type
1	chr11:67370569..67373136-chr17:19651754..19653561,2	MCF-7	breast:
2	chr17:19649191..19653636-chr17:19654131..19659903,8	MCF-7	breast:
3	chr17:19647645..19649705-chr17:19651744..19653267,2	MCF-7	breast:

Variant related genes	Relation type
ALDH3A1	TF binding region
ENSG00000108602	Chromatin interaction
ENSG00000255119	Chromatin interaction
ENSG00000230607	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1006553	0.88[CEU][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1042183	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11650088	0.88[CEU][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11651480	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11653719	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11655457	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11656096	0.82[JPT][hapmap]
rs12945000	0.87[EUR][1000 genomes]
rs12948881	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17720157	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1800869	1.00[YRI][hapmap]
rs1989379	0.84[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs2016823	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2072329	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2072330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3760486	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3786036	0.84[CEU][hapmap];0.95[EUR][1000 genomes]
rs3826507	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv907866	chr17:19582533-19697976	Weak transcription Genic enhancers Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv1807724	chr17:19597423-19656009	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv907867	chr17:19603060-19697976	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	esv1793043	chr17:19604821-19670329	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv457704	chr17:19620477-19663747	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv470582	chr17:19620477-19663747	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv574580	chr17:19620477-19663747	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3760487	ALDH3A2	cis	lymphoblastoid	seeQTL
rs3760487	FLJ10847	cis	multi-tissue	Pritchard
rs3760487	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19648800-19652600	Enhancers	Duodenum Mucosa	Duodenum
2	chr17:19648800-19654200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr17:19648800-19654200	Weak transcription	HUVEC	blood vessel
4	chr17:19648800-19656200	Weak transcription	Aorta	Aorta
5	chr17:19648800-19657000	Weak transcription	Spleen	Spleen
6	chr17:19649000-19652600	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr17:19649000-19656400	Weak transcription	Right Atrium	heart
8	chr17:19649200-19652600	Enhancers	Colonic Mucosa	Colon
9	chr17:19649200-19656200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr17:19649800-19652800	Weak transcription	GM12878-XiMat	blood
11	chr17:19650200-19656800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr17:19650600-19657000	Enhancers	HMEC	breast
13	chr17:19650600-19657600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr17:19651000-19652600	Enhancers	Liver	Liver
15	chr17:19651000-19652600	Flanking Active TSS	Hela-S3	cervix
16	chr17:19651000-19656200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr17:19651200-19652600	Enhancers	Brain Hippocampus Middle	brain
18	chr17:19651200-19652600	Bivalent Enhancer	Fetal Muscle Leg	muscle
19	chr17:19651200-19653400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr17:19651200-19654400	Enhancers	NHEK	skin
21	chr17:19651400-19652600	Enhancers	Stomach Smooth Muscle	stomach
22	chr17:19651600-19652600	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr17:19651600-19652600	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr17:19651600-19652600	Enhancers	NHDF-Ad	bronchial
25	chr17:19651600-19652800	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr17:19651600-19653000	Enhancers	Gastric	stomach
27	chr17:19651600-19654800	Enhancers	Esophagus	oesophagus
28	chr17:19651800-19653400	Enhancers	Stomach Mucosa	stomach
29	chr17:19652000-19652600	Flanking Active TSS	A549	lung
30	chr17:19652000-19653400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr17:19652000-19655400	Weak transcription	HSMMtube	muscle
32	chr17:19652000-19655800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr17:19652200-19652600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr17:19652200-19653600	Enhancers	HepG2	liver
35	chr17:19652200-19654200	Weak transcription	Lung	lung
36	chr17:19652200-19654200	Weak transcription	HSMM	muscle
37	chr17:19652200-19655800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr17:19652200-19655800	Weak transcription	Brain Angular Gyrus	brain
39	chr17:19652200-19656000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr17:19652200-19656000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr17:19652200-19656000	Weak transcription	Osteobl	bone
42	chr17:19652400-19652600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr17:19652400-19652600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr17:19652400-19655400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr17:19652400-19655400	Weak transcription	Brain Substantia Nigra	brain
46	chr17:19652400-19655600	Weak transcription	Adipose Nuclei	Adipose
47	chr17:19652400-19655600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr17:19652400-19655800	Weak transcription	Brain Anterior Caudate	brain
49	chr17:19652400-19655800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr17:19652400-19655800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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