Variant report

Variant	rs11204412
Chromosome Location	chr17:19623971-19623972
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	GTF2F1	chr17:19623878-19624504	Hela-S3	cervix:	n/a	n/a
2	USF1	chr17:19623870-19624562	ECC-1	luminal epithelium:	n/a	chr17:19624212-19624223 chr17:19624213-19624222 chr17:19624214-19624223 chr17:19624211-19624224 chr17:19624207-19624228
3	USF1	chr17:19623766-19624596	ECC-1	luminal epithelium:	n/a	chr17:19624212-19624223 chr17:19624213-19624222 chr17:19624214-19624223 chr17:19624211-19624224 chr17:19624207-19624228
4	ZBTB7A	chr17:19623522-19624751	ECC-1	luminal epithelium:	n/a	n/a
5	BHLHE40	chr17:19623965-19624467	HepG2	liver:	n/a	chr17:19624213-19624222 chr17:19624214-19624223 chr17:19624211-19624224 chr17:19624207-19624228
6	CTCF	chr17:19623920-19624070	RPTEC	kidney:	n/a	n/a
7	MAX	chr17:19623810-19624452	Hela-S3	cervix:	n/a	n/a
8	YY1	chr17:19623072-19624720	ECC-1	luminal epithelium:	n/a	n/a
9	RAD21	chr17:19623962-19624353	Hela-S3	cervix:	n/a	n/a
10	MAX	chr17:19623035-19624610	ECC-1	luminal epithelium:	n/a	chr17:19624504-19624514
11	STAT3	chr17:19623614-19624423	MCF10A-Er-Src	breast:	n/a	chr17:19624131-19624138
12	ESR1	chr17:19622946-19624505	ECC-1	luminal epithelium:	n/a	chr17:19623227-19623242 chr17:19623301-19623316
13	ESR1	chr17:19623101-19624392	ECC-1	luminal epithelium:	n/a	chr17:19623227-19623242 chr17:19623301-19623316
14	BRCA1	chr17:19623902-19624090	Hela-S3	cervix:	n/a	n/a
15	USF1	chr17:19623910-19624482	HCT-116	colon:	n/a	chr17:19624212-19624223 chr17:19624213-19624222 chr17:19624214-19624223 chr17:19624211-19624224 chr17:19624207-19624228
16	CEBPB	chr17:19623938-19624550	ECC-1	luminal epithelium:	n/a	n/a
17	EP300	chr17:19622981-19624687	ECC-1	luminal epithelium:	n/a	chr17:19623022-19623029
18	STAT3	chr17:19623787-19624272	MCF10A-Er-Src	breast:	n/a	chr17:19624131-19624138
19	TEAD4	chr17:19623005-19624707	ECC-1	luminal epithelium:	n/a	n/a
20	TFAP2A	chr17:19623678-19624647	Hela-S3	cervix:	n/a	chr17:19624556-19624570 chr17:19624556-19624570
21	TEAD4	chr17:19622607-19624645	ECC-1	luminal epithelium:	n/a	n/a
22	NR3C1	chr17:19623910-19624377	ECC-1	luminal epithelium:	n/a	chr17:19624366-19624375
23	FOS	chr17:19623813-19624401	MCF10A-Er-Src	breast:	n/a	n/a
24	SMC3	chr17:19623824-19624455	Hela-S3	cervix:	n/a	chr17:19623960-19623970
25	ZBTB7A	chr17:19622788-19624774	ECC-1	luminal epithelium:	n/a	chr17:19622910-19622918 chr17:19622983-19622997 chr17:19622984-19622998 chr17:19622911-19622919
26	POLR2A	chr17:19623923-19624316	Hela-S3	cervix:	n/a	n/a
27	TCF7L2	chr17:19623620-19624476	Hela-S3	cervix:	n/a	n/a
28	NFIC	chr17:19622613-19624764	ECC-1	luminal epithelium:	n/a	chr17:19624229-19624246 chr17:19624230-19624246
29	TCF12	chr17:19622858-19624837	ECC-1	luminal epithelium:	n/a	chr17:19624809-19624816 chr17:19624811-19624818
30	YY1	chr17:19623152-19624566	ECC-1	luminal epithelium:	n/a	n/a
31	MAX	chr17:19623016-19624864	ECC-1	luminal epithelium:	n/a	chr17:19624504-19624514
32	ESR1	chr17:19622971-19624446	ECC-1	luminal epithelium:	n/a	chr17:19623227-19623242 chr17:19623301-19623316
33	EP300	chr17:19622762-19624918	ECC-1	luminal epithelium:	n/a	chr17:19623022-19623029
34	FOXM1	chr17:19623029-19624701	ECC-1	luminal epithelium:	n/a	n/a
35	NFIC	chr17:19622501-19624942	ECC-1	luminal epithelium:	n/a	chr17:19624229-19624246 chr17:19624230-19624246
36	FOXM1	chr17:19622946-19624798	ECC-1	luminal epithelium:	n/a	n/a
37	TFAP2C	chr17:19622515-19624604	Hela-S3	cervix:	n/a	n/a
38	TCF12	chr17:19623013-19624857	ECC-1	luminal epithelium:	n/a	chr17:19624809-19624816 chr17:19624811-19624818
39	ESR1	chr17:19622953-19624569	ECC-1	luminal epithelium:	n/a	chr17:19623227-19623242 chr17:19623301-19623316
40	NR3C1	chr17:19623887-19624464	ECC-1	luminal epithelium:	n/a	chr17:19624366-19624375
41	RAD21	chr17:19623104-19624565	ECC-1	luminal epithelium:	n/a	chr17:19624501-19624511 chr17:19624516-19624525 chr17:19623819-19623838
42	MYC	chr17:19623857-19624320	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19623453..19625417-chr17:19651526..19653973,2	MCF-7	breast:
2	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
ENSG00000180638	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1006554	0.89[EUR][1000 genomes]
rs11204411	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.95[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	0.86[EUR][1000 genomes]
rs12942065	0.81[CEU][hapmap]
rs12945122	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12948735	0.88[EUR][1000 genomes]
rs2010728	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2108967	0.90[GIH][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs4646787	0.90[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs4924793	0.89[EUR][1000 genomes]
rs7209418	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]
rs7214841	0.92[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs7221211	0.87[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs7222877	1.00[CEU][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes]
rs8077368	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs887241	0.90[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs9910370	0.96[CEU][hapmap];0.91[TSI][hapmap];0.95[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11204412	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL
rs11204412	ALDH3A2	cis	cerebellum	SCAN
rs11204412	EPN2	cis	parietal	SCAN

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

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	chr17:19619400-19624800	Enhancers	Esophagus	oesophagus
4	chr17:19619400-19625000	Enhancers	Fetal Muscle Leg	muscle
5	chr17:19619600-19625000	Enhancers	HMEC	breast
6	chr17:19619800-19627800	Enhancers	Fetal Intestine Large	intestine
7	chr17:19620000-19624800	Enhancers	HSMMtube	muscle
8	chr17:19620000-19628000	Enhancers	Fetal Intestine Small	intestine
9	chr17:19620200-19624800	Enhancers	Stomach Mucosa	stomach
10	chr17:19620400-19625000	Enhancers	Colonic Mucosa	Colon
11	chr17:19620600-19627400	Weak transcription	Brain Anterior Caudate	brain
12	chr17:19620800-19624800	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr17:19621200-19624800	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr17:19621600-19624400	Enhancers	Placenta	Placenta
15	chr17:19621600-19624600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr17:19622200-19624000	Enhancers	HepG2	liver
17	chr17:19622400-19624600	Enhancers	Ovary	ovary
18	chr17:19622600-19625000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr17:19622800-19624600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr17:19622800-19624800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr17:19622800-19624800	Enhancers	NHEK	skin
22	chr17:19623000-19624200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr17:19623000-19624800	Enhancers	Gastric	stomach
24	chr17:19623000-19624800	Enhancers	Lung	lung
25	chr17:19623000-19624800	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr17:19623000-19625200	Enhancers	A549	lung
27	chr17:19623200-19624000	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr17:19623200-19624000	Enhancers	Small Intestine	intestine
29	chr17:19623200-19624400	Flanking Active TSS	Hela-S3	cervix
30	chr17:19623200-19624600	Enhancers	Pancreas	Pancrea
31	chr17:19623200-19624800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr17:19623200-19648400	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr17:19623400-19624200	Enhancers	Fetal Lung	lung
34	chr17:19623400-19624400	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr17:19623400-19624400	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr17:19623400-19624400	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr17:19623400-19624600	Enhancers	Adipose Nuclei	Adipose
38	chr17:19623400-19624600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
39	chr17:19623400-19628000	Enhancers	Fetal Heart	heart
40	chr17:19623600-19624000	Enhancers	Stomach Smooth Muscle	stomach
41	chr17:19623600-19624600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr17:19623600-19624600	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr17:19623600-19624800	Enhancers	Spleen	Spleen
44	chr17:19623600-19625200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr17:19623800-19624400	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr17:19623800-19624400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr17:19623800-19624400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr17:19623800-19624400	Enhancers	Left Ventricle	heart
49	chr17:19623800-19624600	Enhancers	Right Ventricle	heart
50	chr17:19623800-19625200	Enhancers	Fetal Kidney	kidney

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