Variant report

Variant	rs12945000
Chromosome Location	chr17:19627822-19627823
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:19551445..19552984-chr17:19627391..19629218,2	MCF-7	breast:
2	chr17:19627784..19630174-chr17:19639467..19641873,3	MCF-7	breast:
3	chr11:67380566..67382466-chr17:19627123..19628760,2	MCF-7	breast:
4	chr17:19627605..19629507-chr17:19658894..19661026,2	MCF-7	breast:
5	chr17:19551299..19553745-chr17:19626814..19628923,2	MCF-7	breast:
6	chr17:19625321..19633420-chr17:19643892..19652817,11	MCF-7	breast:
7	chr17:19624830..19631833-chr17:19654160..19660410,12	MCF-7	breast:
8	chr17:19626221..19628262-chr17:19634519..19636560,2	MCF-7	breast:
9	chr17:19617480..19620219-chr17:19627311..19629602,2	MCF-7	breast:
10	chr17:19626307..19628911-chr8:125486241..125488488,2	MCF-7	breast:
11	chr17:19627403..19631543-chr17:19639531..19642900,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000231793	Chromatin interaction
ENSG00000072210	Chromatin interaction
ENSG00000245149	Chromatin interaction
ENSG00000170881	Chromatin interaction
ENSG00000230607	Chromatin interaction
ENSG00000180638	Chromatin interaction
ENSG00000264785	Chromatin interaction
ENSG00000108602	Chromatin interaction
ENSG00000264932	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1006553	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1042183	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11650088	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11651480	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11653719	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11655457	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655989	0.80[ASN][1000 genomes]
rs11656096	0.81[ASN][1000 genomes]
rs11657205	0.81[EUR][1000 genomes]
rs12948881	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17720157	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1989379	0.92[EUR][1000 genomes]
rs2016823	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2072329	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2072330	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34834489	0.81[ASN][1000 genomes]
rs3760486	0.87[EUR][1000 genomes]
rs3760487	0.87[EUR][1000 genomes]
rs3786036	0.84[EUR][1000 genomes]
rs3826507	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
12	esv3406151	chr17:19626085-19628158	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12945000	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 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	chr17:19620000-19628000	Enhancers	Fetal Intestine Small	intestine
3	chr17:19623200-19648400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:19623400-19628000	Enhancers	Fetal Heart	heart
5	chr17:19624000-19630600	Weak transcription	Small Intestine	intestine
6	chr17:19624800-19631400	Weak transcription	Brain Germinal Matrix	brain
7	chr17:19625000-19630800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr17:19625200-19631000	Weak transcription	Fetal Kidney	kidney
9	chr17:19625800-19630400	Weak transcription	HepG2	liver
10	chr17:19626400-19628000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr17:19626400-19628800	Enhancers	Fetal Muscle Leg	muscle
12	chr17:19626600-19629000	Enhancers	HMEC	breast
13	chr17:19627000-19629000	Enhancers	A549	lung
14	chr17:19627200-19628200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr17:19627200-19628200	Flanking Active TSS	NHEK	skin
16	chr17:19627200-19628400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr17:19627200-19628600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr17:19627200-19628600	Enhancers	Fetal Muscle Trunk	muscle
19	chr17:19627200-19628800	Enhancers	Primary hematopoietic stem cells	blood
20	chr17:19627200-19628800	Enhancers	Placenta	Placenta
21	chr17:19627200-19628800	Enhancers	Right Ventricle	heart
22	chr17:19627200-19629200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr17:19627400-19628000	Enhancers	Brain Substantia Nigra	brain
24	chr17:19627400-19628000	Enhancers	Esophagus	oesophagus
25	chr17:19627400-19628000	Enhancers	Left Ventricle	heart
26	chr17:19627400-19628000	Enhancers	Psoas Muscle	Psoas
27	chr17:19627400-19628000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr17:19627400-19628200	Enhancers	Liver	Liver
29	chr17:19627400-19628200	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr17:19627400-19628400	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr17:19627400-19628600	Enhancers	Gastric	stomach
32	chr17:19627400-19628600	Enhancers	Lung	lung
33	chr17:19627400-19628600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr17:19627400-19628600	Enhancers	Spleen	Spleen
35	chr17:19627400-19629000	Enhancers	Primary B cells from cord blood	blood
36	chr17:19627400-19629000	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr17:19627400-19629200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr17:19627400-19629200	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr17:19627600-19628000	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr17:19627600-19628000	Flanking Active TSS	Primary B cells from peripheral blood	blood
41	chr17:19627600-19628000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr17:19627600-19628000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr17:19627600-19628000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr17:19627600-19628000	Active TSS	Brain Angular Gyrus	brain
45	chr17:19627600-19628000	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr17:19627600-19628000	Flanking Active TSS	Stomach Mucosa	stomach
47	chr17:19627600-19628000	Enhancers	HSMM	muscle
48	chr17:19627600-19628200	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr17:19627600-19628200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr17:19627600-19628200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin

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