Variant report

Variant	rs2072327
Chromosome Location	chr17:19651482-19651483
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	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	JUND	chr17:19649752-19652440	A549	lung:	n/a	chr17:19652091-19652103 chr17:19652089-19652100
4	CEBPB	chr17:19651285-19652664	A549	lung:	n/a	n/a
5	ZBTB33	chr17:19650426-19652363	A549	lung:	n/a	n/a
6	TCF12	chr17:19650454-19652262	A549	lung:	n/a	chr17:19651904-19651912
7	FOXA2	chr17:19650836-19652908	A549	lung:	n/a	n/a
8	TAF1	chr17:19650416-19652480	A549	lung:	n/a	n/a
9	TCF7L2	chr17:19651443-19652064	MCF-7	breast:	n/a	n/a
10	REST	chr17:19649555-19652980	A549	lung:	n/a	chr17:19650573-19650591 chr17:19652049-19652062 chr17:19652019-19652029
11	TCF12	chr17:19647575-19653308	A549	lung:	n/a	chr17:19648161-19648171 chr17:19648468-19648475 chr17:19648978-19648985 chr17:19651904-19651912
12	POLR2A	chr17:19650477-19651757	A549	lung:	n/a	n/a
13	SIX5	chr17:19650107-19653086	A549	lung:	n/a	n/a
14	SIN3AK20	chr17:19650460-19652543	A549	lung:	n/a	n/a
15	POLR2A	chr17:19649543-19652557	A549	lung:	n/a	n/a
16	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
17	ZBTB7A	chr17:19651350-19652402	ECC-1	luminal epithelium:	n/a	n/a
18	TCF12	chr17:19651355-19652894	ECC-1	luminal epithelium:	n/a	chr17:19651904-19651912
19	NR3C1	chr17:19650631-19652321	A549	lung:	n/a	chr17:19650710-19650717
20	FOXA2	chr17:19650548-19652534	A549	lung:	n/a	n/a
21	E2F6	chr17:19650119-19653193	A549	lung:	n/a	chr17:19652359-19652371
22	ETS1	chr17:19650619-19652279	A549	lung:	n/a	n/a
23	CTCF	chr17:19647746-19653300	A549	lung:	n/a	chr17:19648889-19648902 chr17:19650591-19650599 chr17:19651387-19651397 chr17:19649367-19649376
24	MAX	chr17:19651150-19652545	A549	lung:	n/a	chr17:19651879-19651888
25	POLR2A	chr17:19650474-19651812	A549	lung:	n/a	n/a
26	EP300	chr17:19651449-19652603	ECC-1	luminal epithelium:	n/a	chr17:19651868-19651878 chr17:19651785-19651795
27	RFX5	chr17:19651332-19652088	Hela-S3	cervix:	n/a	n/a
28	RAD21	chr17:19651236-19652162	A549	lung:	n/a	chr17:19651386-19651396
29	ATF3	chr17:19650727-19652245	A549	lung:	n/a	n/a
30	ELF1	chr17:19649892-19652087	A549	lung:	n/a	chr17:19650152-19650163
31	ZBTB33	chr17:19650486-19652351	A549	lung:	n/a	n/a
32	GABPA	chr17:19651442-19652015	A549	lung:	n/a	n/a
33	RCOR1	chr17:19651367-19651984	Hela-S3	cervix:	n/a	n/a
34	NR3C1	chr17:19651171-19652186	A549	lung:	n/a	n/a
35	MAX	chr17:19648056-19653846	A549	lung:	n/a	chr17:19651879-19651888 chr17:19648221-19648230 chr17:19648968-19648984
36	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
37	TCF12	chr17:19651421-19652649	ECC-1	luminal epithelium:	n/a	chr17:19651904-19651912
38	USF1	chr17:19649934-19652251	A549	lung:	n/a	n/a
39	EP300	chr17:19651454-19652862	ECC-1	luminal epithelium:	n/a	chr17:19651868-19651878 chr17:19652732-19652741 chr17:19651785-19651795
40	PBX3	chr17:19650471-19652146	A549	lung:	n/a	n/a
41	TEAD4	chr17:19651348-19652378	A549	lung:	n/a	n/a
42	EP300	chr17:19649666-19653003	A549	lung:	n/a	chr17:19650306-19650322 chr17:19651055-19651065 chr17:19651868-19651878 chr17:19652732-19652741 chr17:19651785-19651795
43	FOSL2	chr17:19648208-19652390	A549	lung:	n/a	chr17:19652091-19652103 chr17:19648607-19648618 chr17:19652089-19652100
44	CREB1	chr17:19651122-19652286	A549	lung:	n/a	n/a
45	POLR2A	chr17:19647758-19651715	A549	lung:	n/a	n/a
46	TEAD4	chr17:19651306-19652166	A549	lung:	n/a	n/a
47	FOXM1	chr17:19651455-19652690	ECC-1	luminal epithelium:	n/a	n/a
48	CREB1	chr17:19651458-19651974	A549	lung:	n/a	n/a
49	GABPA	chr17:19651085-19652352	A549	lung:	n/a	n/a
50	ATF3	chr17:19650542-19652172	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:19641924..19645093-chr17:19650303..19652085,4	MCF-7	breast:
2	chr11:67372115..67374476-chr17:19649917..19652325,2	MCF-7	breast:
3	chr17:19649191..19653636-chr17:19654131..19659903,8	MCF-7	breast:

Variant related genes	Relation type
ALDH3A1	TF binding region
ENSG00000184224	Chromatin interaction
ENSG00000230607	Chromatin interaction
ENSG00000167792	Chromatin interaction
ENSG00000255119	Chromatin interaction
ENSG00000108602	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1006556	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12939864	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12949049	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16960360	0.94[JPT][hapmap]
rs2228100	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3786036	0.83[CHB][hapmap]
rs4646785	0.81[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4925045	0.89[JPT][hapmap]
rs9897570	0.80[JPT][hapmap]
rs9900497	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv526290	chr17:19613357-19651482	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2072327	ALDH3A2	cis	multi-tissue	Pritchard
rs2072327	FLJ10847	cis	multi-tissue	Pritchard

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19648600-19651600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr17:19648600-19651800	Weak transcription	HSMM	muscle
3	chr17:19648800-19652200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr17:19648800-19652600	Enhancers	Duodenum Mucosa	Duodenum
5	chr17:19648800-19654200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr17:19648800-19654200	Weak transcription	HUVEC	blood vessel
7	chr17:19648800-19656200	Weak transcription	Aorta	Aorta
8	chr17:19648800-19657000	Weak transcription	Spleen	Spleen
9	chr17:19649000-19651600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr17:19649000-19651600	Weak transcription	Pancreas	Pancrea
11	chr17:19649000-19652600	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr17:19649000-19656400	Weak transcription	Right Atrium	heart
13	chr17:19649200-19651600	Weak transcription	Adipose Nuclei	Adipose
14	chr17:19649200-19651600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr17:19649200-19652600	Enhancers	Colonic Mucosa	Colon
16	chr17:19649200-19656200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr17:19649400-19651600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr17:19649800-19652800	Weak transcription	GM12878-XiMat	blood
19	chr17:19650200-19651600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr17:19650200-19656800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr17:19650600-19651600	Flanking Active TSS	Esophagus	oesophagus
22	chr17:19650600-19657000	Enhancers	HMEC	breast
23	chr17:19650600-19657600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr17:19650800-19652400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr17:19651000-19652200	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr17:19651000-19652400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
27	chr17:19651000-19652400	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr17:19651000-19652600	Enhancers	Liver	Liver
29	chr17:19651000-19652600	Flanking Active TSS	Hela-S3	cervix
30	chr17:19651000-19656200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr17:19651200-19651600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr17:19651200-19651600	Enhancers	Brain Substantia Nigra	brain
33	chr17:19651200-19651600	Flanking Active TSS	Gastric	stomach
34	chr17:19651200-19651800	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
35	chr17:19651200-19651800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr17:19651200-19652200	Enhancers	Fetal Intestine Small	intestine
37	chr17:19651200-19652200	Flanking Active TSS	HepG2	liver
38	chr17:19651200-19652400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr17:19651200-19652400	Enhancers	Brain Cingulate Gyrus	brain
40	chr17:19651200-19652600	Enhancers	Brain Hippocampus Middle	brain
41	chr17:19651200-19652600	Bivalent Enhancer	Fetal Muscle Leg	muscle
42	chr17:19651200-19653400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr17:19651200-19654400	Enhancers	NHEK	skin
44	chr17:19651400-19651600	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr17:19651400-19651600	Flanking Active TSS	A549	lung
46	chr17:19651400-19651800	Active TSS	Stomach Mucosa	stomach
47	chr17:19651400-19652000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr17:19651400-19652000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr17:19651400-19652000	Bivalent Enhancer	Fetal Intestine Large	intestine
50	chr17:19651400-19652000	Weak transcription	Lung	lung

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