Variant report

Variant	rs7209418
Chromosome Location	chr17:19624838-19624839
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	MAX	chr17:19623016-19624864	ECC-1	luminal epithelium:	n/a	chr17:19624504-19624514
2	EP300	chr17:19622762-19624918	ECC-1	luminal epithelium:	n/a	chr17:19623022-19623029
3	NFIC	chr17:19622501-19624942	ECC-1	luminal epithelium:	n/a	chr17:19624229-19624246 chr17:19624230-19624246
4	TCF12	chr17:19623013-19624857	ECC-1	luminal epithelium:	n/a	chr17:19624809-19624816 chr17:19624811-19624818

No.	Distal block	Cell Line	Cell type
1	chr17:19623453..19625417-chr17:19651526..19653973,2	MCF-7	breast:
2	chr17:19624830..19631833-chr17:19654160..19660410,12	MCF-7	breast:
3	chr17:19617555..19619828-chr17:19622180..19625084,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ALDH3A2-1	chr17:19622372-19625741	ENSG00000262681.2

Variant related genes	Relation type
SLC47A2	TF binding region
ENSG00000108602	Chromatin interaction
ENSG00000230607	Chromatin interaction
ENSG00000180638	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1006554	0.90[EUR][1000 genomes]
rs11204411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204413	0.96[EUR][1000 genomes]
rs11204414	0.87[EUR][1000 genomes]
rs12942065	0.81[CEU][hapmap]
rs12945122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12948735	0.89[EUR][1000 genomes]
rs2010728	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2108967	0.88[EUR][1000 genomes]
rs4646787	0.84[EUR][1000 genomes]
rs4924793	0.90[EUR][1000 genomes]
rs7214841	0.91[CEU][hapmap];0.96[EUR][1000 genomes]
rs7221211	0.85[EUR][1000 genomes]
rs7222877	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs8077368	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs887241	0.85[EUR][1000 genomes]
rs9910370	0.96[CEU][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482827	chr17:19456848-19645771	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7209418	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19607600-19627400	Weak transcription	Right Atrium	heart
2	chr17:19617600-19635400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr17:19619400-19625000	Enhancers	Fetal Muscle Leg	muscle
4	chr17:19619600-19625000	Enhancers	HMEC	breast
5	chr17:19619800-19627800	Enhancers	Fetal Intestine Large	intestine
6	chr17:19620000-19628000	Enhancers	Fetal Intestine Small	intestine
7	chr17:19620400-19625000	Enhancers	Colonic Mucosa	Colon
8	chr17:19620600-19627400	Weak transcription	Brain Anterior Caudate	brain
9	chr17:19622600-19625000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr17:19623000-19625200	Enhancers	A549	lung
11	chr17:19623200-19648400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr17:19623400-19628000	Enhancers	Fetal Heart	heart
13	chr17:19623600-19625200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr17:19623800-19625200	Enhancers	Fetal Kidney	kidney
15	chr17:19624000-19627600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr17:19624000-19630600	Weak transcription	Small Intestine	intestine
17	chr17:19624200-19625000	Enhancers	Fetal Muscle Trunk	muscle
18	chr17:19624200-19627400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr17:19624200-19627800	Weak transcription	Fetal Lung	lung
20	chr17:19624400-19625200	Enhancers	Hela-S3	cervix
21	chr17:19624400-19626400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr17:19624400-19626600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr17:19624400-19627200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr17:19624400-19627200	Weak transcription	Placenta	Placenta
25	chr17:19624400-19627200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr17:19624400-19627200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr17:19624400-19627200	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr17:19624400-19627400	Weak transcription	Left Ventricle	heart
29	chr17:19624600-19625600	Enhancers	Duodenum Mucosa	Duodenum
30	chr17:19624600-19625800	Enhancers	HepG2	liver
31	chr17:19624600-19626200	Weak transcription	Right Ventricle	heart
32	chr17:19624600-19626400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr17:19624600-19626400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr17:19624600-19627200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr17:19624600-19627200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr17:19624600-19627400	Weak transcription	Adipose Nuclei	Adipose
37	chr17:19624600-19627400	Weak transcription	Liver	Liver
38	chr17:19624600-19627400	Weak transcription	Ovary	ovary
39	chr17:19624600-19627600	Weak transcription	Pancreas	Pancrea
40	chr17:19624800-19626400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr17:19624800-19626400	Weak transcription	NHEK	skin
42	chr17:19624800-19627400	Weak transcription	Esophagus	oesophagus
43	chr17:19624800-19627400	Weak transcription	Gastric	stomach
44	chr17:19624800-19627400	Weak transcription	Lung	lung
45	chr17:19624800-19627400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr17:19624800-19627400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr17:19624800-19627400	Weak transcription	Stomach Mucosa	stomach
48	chr17:19624800-19627400	Weak transcription	Spleen	Spleen
49	chr17:19624800-19627400	Weak transcription	HSMMtube	muscle
50	chr17:19624800-19627600	Weak transcription	Rectal Mucosa Donor 29	rectum

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