Variant report

Variant	rs11204413
Chromosome Location	chr17:19630353-19630354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:67397332..67399717-chr17:19628454..19630987,2	MCF-7	breast:
2	chr17:19625321..19633420-chr17:19643892..19652817,11	MCF-7	breast:
3	chr17:19624830..19631833-chr17:19654160..19660410,12	MCF-7	breast:
4	chr17:19618336..19623572-chr17:19629964..19633338,7	MCF-7	breast:
5	chr17:19627403..19631543-chr17:19639531..19642900,3	MCF-7	breast:
6	chr11:67379967..67381601-chr17:19627957..19630440,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108602	Chromatin interaction
ENSG00000230607	Chromatin interaction
ENSG00000262681	Chromatin interaction
ENSG00000264785	Chromatin interaction
ENSG00000167799	Chromatin interaction
ENSG00000180638	Chromatin interaction
ENSG00000231793	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1006554	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204411	0.96[EUR][1000 genomes]
rs11204412	0.96[EUR][1000 genomes]
rs11204414	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12942065	0.93[ASN][1000 genomes]
rs12945122	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12948209	0.93[ASN][1000 genomes]
rs12948735	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010728	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2108967	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3744693	0.90[ASN][1000 genomes]
rs4646787	0.87[EUR][1000 genomes]
rs4924793	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925044	0.93[ASN][1000 genomes]
rs7209418	0.96[EUR][1000 genomes]
rs7212752	0.88[ASN][1000 genomes]
rs7214841	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7221211	0.87[EUR][1000 genomes]
rs7222877	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8064572	0.90[ASN][1000 genomes]
rs8073794	0.83[ASN][1000 genomes]
rs8077368	0.91[EUR][1000 genomes]
rs887241	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9910370	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][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
rs11204413	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19617600-19635400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr17:19623200-19648400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr17:19624000-19630600	Weak transcription	Small Intestine	intestine
4	chr17:19624800-19631400	Weak transcription	Brain Germinal Matrix	brain
5	chr17:19625000-19630800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr17:19625200-19631000	Weak transcription	Fetal Kidney	kidney
7	chr17:19625800-19630400	Weak transcription	HepG2	liver
8	chr17:19628000-19630600	Weak transcription	Left Ventricle	heart
9	chr17:19628000-19630600	Weak transcription	HSMM	muscle
10	chr17:19628000-19630800	Weak transcription	Fetal Heart	heart
11	chr17:19628200-19630400	Weak transcription	Liver	Liver
12	chr17:19628200-19640800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr17:19628400-19630400	Weak transcription	Fetal Lung	lung
14	chr17:19628400-19630600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr17:19628400-19630600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr17:19628400-19630600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr17:19628400-19630600	Weak transcription	Psoas Muscle	Psoas
18	chr17:19628600-19630400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr17:19628600-19630400	Weak transcription	Pancreas	Pancrea
20	chr17:19628600-19630400	Weak transcription	Spleen	Spleen
21	chr17:19628600-19630600	Weak transcription	Esophagus	oesophagus
22	chr17:19628600-19630600	Weak transcription	Lung	lung
23	chr17:19628600-19631000	Weak transcription	Fetal Intestine Large	intestine
24	chr17:19628600-19631000	Weak transcription	Gastric	stomach
25	chr17:19628600-19631200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr17:19628800-19630400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr17:19628800-19630600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr17:19628800-19630600	Weak transcription	Fetal Intestine Small	intestine
29	chr17:19628800-19630600	Weak transcription	Placenta	Placenta
30	chr17:19628800-19630600	Weak transcription	Stomach Mucosa	stomach
31	chr17:19628800-19630800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr17:19628800-19631000	Weak transcription	HUVEC	blood vessel
33	chr17:19629200-19630400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr17:19629200-19630400	Weak transcription	Colonic Mucosa	Colon
35	chr17:19629200-19633800	Enhancers	Fetal Muscle Leg	muscle
36	chr17:19629400-19630600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr17:19629400-19630800	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr17:19629400-19631000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr17:19629400-19632000	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr17:19629400-19632200	Enhancers	Colon Smooth Muscle	Colon
41	chr17:19629600-19630600	Weak transcription	Fetal Muscle Trunk	muscle
42	chr17:19629800-19630600	Enhancers	Adipose Nuclei	Adipose
43	chr17:19629800-19631000	Enhancers	Brain Hippocampus Middle	brain
44	chr17:19629800-19632200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr17:19629800-19632200	Enhancers	Muscle Satellite Cultured Cells	--
46	chr17:19629800-19632200	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr17:19629800-19633200	Enhancers	Brain Substantia Nigra	brain
48	chr17:19630000-19631000	Enhancers	Brain Anterior Caudate	brain
49	chr17:19630000-19631000	Enhancers	Brain Cingulate Gyrus	brain
50	chr17:19630000-19631000	Enhancers	Rectal Smooth Muscle	rectum

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