Variant report

Variant	rs57629792
Chromosome Location	chr17:19625298-19625299
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	STAT3	chr17:19625003-19625646	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	chr17:19624830..19631833-chr17:19654160..19660410,12	MCF-7	breast:

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

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12325921	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16960382	1.00[AMR][1000 genomes]
rs16960386	1.00[AMR][1000 genomes]
rs28552545	1.00[AMR][1000 genomes]
rs7213030	1.00[AMR][1000 genomes]
rs9901772	0.81[AFR][1000 genomes]
rs9901778	0.90[AFR][1000 genomes]
rs9915956	0.93[AFR][1000 genomes];1.00[AMR][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

No data

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	chr17:19619800-19627800	Enhancers	Fetal Intestine Large	intestine
4	chr17:19620000-19628000	Enhancers	Fetal Intestine Small	intestine
5	chr17:19620600-19627400	Weak transcription	Brain Anterior Caudate	brain
6	chr17:19623200-19648400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr17:19623400-19628000	Enhancers	Fetal Heart	heart
8	chr17:19624000-19627600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr17:19624000-19630600	Weak transcription	Small Intestine	intestine
10	chr17:19624200-19627400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr17:19624200-19627800	Weak transcription	Fetal Lung	lung
12	chr17:19624400-19626400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr17:19624400-19626600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr17:19624400-19627200	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr17:19624400-19627200	Weak transcription	Placenta	Placenta
16	chr17:19624400-19627200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr17:19624400-19627200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr17:19624400-19627200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr17:19624400-19627400	Weak transcription	Left Ventricle	heart
20	chr17:19624600-19625600	Enhancers	Duodenum Mucosa	Duodenum
21	chr17:19624600-19625800	Enhancers	HepG2	liver
22	chr17:19624600-19626200	Weak transcription	Right Ventricle	heart
23	chr17:19624600-19626400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr17:19624600-19626400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr17:19624600-19627200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr17:19624600-19627200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr17:19624600-19627400	Weak transcription	Adipose Nuclei	Adipose
28	chr17:19624600-19627400	Weak transcription	Liver	Liver
29	chr17:19624600-19627400	Weak transcription	Ovary	ovary
30	chr17:19624600-19627600	Weak transcription	Pancreas	Pancrea
31	chr17:19624800-19626400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr17:19624800-19626400	Weak transcription	NHEK	skin
33	chr17:19624800-19627400	Weak transcription	Esophagus	oesophagus
34	chr17:19624800-19627400	Weak transcription	Gastric	stomach
35	chr17:19624800-19627400	Weak transcription	Lung	lung
36	chr17:19624800-19627400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr17:19624800-19627400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr17:19624800-19627400	Weak transcription	Stomach Mucosa	stomach
39	chr17:19624800-19627400	Weak transcription	Spleen	Spleen
40	chr17:19624800-19627400	Weak transcription	HSMMtube	muscle
41	chr17:19624800-19627600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr17:19624800-19627800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr17:19624800-19631400	Weak transcription	Brain Germinal Matrix	brain
44	chr17:19625000-19626400	Weak transcription	Fetal Muscle Leg	muscle
45	chr17:19625000-19626600	Weak transcription	HMEC	breast
46	chr17:19625000-19627400	Weak transcription	Colonic Mucosa	Colon
47	chr17:19625000-19630800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr17:19625200-19626400	Weak transcription	A549	lung
49	chr17:19625200-19626400	Weak transcription	Hela-S3	cervix
50	chr17:19625200-19631000	Weak transcription	Fetal Kidney	kidney

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