Variant report

Variant	rs12943590
Chromosome Location	chr17:19619998-19619999
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	NR3C1	chr17:19619732-19620070	ECC-1	luminal epithelium:	n/a	n/a
2	ESR1	chr17:19619471-19620389	ECC-1	luminal epithelium:	n/a	chr17:19620217-19620232
3	ESR1	chr17:19619536-19620462	ECC-1	luminal epithelium:	n/a	chr17:19620217-19620232
4	MAX	chr17:19619615-19620280	ECC-1	luminal epithelium:	n/a	n/a
5	EP300	chr17:19619506-19620555	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr17:19619684-19620224	ECC-1	luminal epithelium:	n/a	n/a
7	ESR1	chr17:19619655-19620020	ECC-1	luminal epithelium:	n/a	n/a
8	EP300	chr17:19619524-19620376	ECC-1	luminal epithelium:	n/a	n/a
9	CTCF	chr17:19619960-19620110	HepG2	liver:	n/a	n/a
10	TCF12	chr17:19619479-19621400	ECC-1	luminal epithelium:	n/a	chr17:19619595-19619605
11	TCF12	chr17:19619472-19621437	ECC-1	luminal epithelium:	n/a	chr17:19619595-19619605
12	NR3C1	chr17:19619694-19620061	ECC-1	luminal epithelium:	n/a	n/a
13	ZBTB7A	chr17:19619522-19620237	ECC-1	luminal epithelium:	n/a	n/a
14	ESR1	chr17:19619664-19620164	ECC-1	luminal epithelium:	n/a	n/a
15	ESR1	chr17:19619582-19620346	ECC-1	luminal epithelium:	n/a	chr17:19620217-19620232
16	NFIC	chr17:19619616-19620388	ECC-1	luminal epithelium:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ALDH3A1-1	chr17:19619037-19622150	NONHSAT146520

Variant related genes	Relation type
ENSG00000262681	TF binding region
SLC47A2	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1006556	0.82[ASN][1000 genomes]
rs12451902	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960360	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35263947	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4924792	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925045	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs758426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs758427	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9897570	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9900497	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19607600-19627400	Weak transcription	Right Atrium	heart
2	chr17:19616200-19621400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr17:19617600-19635400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr17:19618200-19620600	Weak transcription	Gastric	stomach
5	chr17:19618200-19623200	Weak transcription	Pancreas	Pancrea
6	chr17:19618400-19620000	Weak transcription	Fetal Intestine Small	intestine
7	chr17:19618400-19620600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr17:19618600-19620200	Active TSS	Brain Anterior Caudate	brain
9	chr17:19618600-19620200	Weak transcription	Stomach Mucosa	stomach
10	chr17:19618600-19620400	Weak transcription	Colonic Mucosa	Colon
11	chr17:19619400-19620200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr17:19619400-19620600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr17:19619400-19620800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr17:19619400-19622200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr17:19619400-19622200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr17:19619400-19622400	Enhancers	A549	lung
17	chr17:19619400-19622800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr17:19619400-19624800	Enhancers	Esophagus	oesophagus
19	chr17:19619400-19625000	Enhancers	Fetal Muscle Leg	muscle
20	chr17:19619600-19620000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr17:19619600-19620000	Active TSS	HSMMtube	muscle
22	chr17:19619600-19620200	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr17:19619600-19620400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr17:19619600-19620400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr17:19619600-19621600	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr17:19619600-19621800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr17:19619600-19622200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr17:19619600-19622200	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr17:19619600-19625000	Enhancers	HMEC	breast
30	chr17:19619800-19620000	Active TSS	Spleen	Spleen
31	chr17:19619800-19620200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr17:19619800-19620200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr17:19619800-19620200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr17:19619800-19620200	Flanking Active TSS	HepG2	liver
35	chr17:19619800-19620200	Enhancers	HSMM	muscle
36	chr17:19619800-19622000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr17:19619800-19622000	Enhancers	NHEK	skin
38	chr17:19619800-19627800	Enhancers	Fetal Intestine Large	intestine

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