Variant report

Variant	rs58690840
Chromosome Location	chr17:16922685-16922686
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr17:16921456-16922833	ECC-1	luminal epithelium:	n/a	chr17:16921474-16921481

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:16920777..16926602-chr17:16943525..16948995,8	MCF-7	breast:
2	chr17:16922009..16924326-chr17:16949178..16951661,2	MCF-7	breast:
3	chr17:16921692..16923812-chr17:17738364..17740042,2	MCF-7	breast:
4	chr17:16920975..16923605-chr17:16945817..16947937,2	K562	blood:
5	chr17:16919740..16922736-chr17:16924450..16926205,2	MCF-7	breast:
6	chr17:16921667..16924582-chr17:17139472..17141116,2	MCF-7	breast:
7	chr17:16920470..16922796-chr17:16981423..16984163,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000260328	TF binding region
ENSG00000133030	Chromatin interaction
ENSG00000154803	Chromatin interaction
ENSG00000264187	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10048152	1.00[EUR][1000 genomes]
rs1131632	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16961406	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28829096	1.00[EUR][1000 genomes]
rs4485421	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55792503	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56247606	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56343767	1.00[EUR][1000 genomes]
rs56912118	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58169814	1.00[EUR][1000 genomes]
rs58377774	0.82[AFR][1000 genomes]
rs58442149	1.00[EUR][1000 genomes]
rs58702370	1.00[EUR][1000 genomes]
rs60029796	1.00[EUR][1000 genomes]
rs60192272	1.00[EUR][1000 genomes]
rs60332371	1.00[EUR][1000 genomes]
rs60364428	1.00[EUR][1000 genomes]
rs60545734	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60697210	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60890438	1.00[EUR][1000 genomes]
rs61024568	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61218165	1.00[EUR][1000 genomes]
rs61608940	1.00[EUR][1000 genomes]
rs7219836	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7223145	1.00[EUR][1000 genomes]
rs7223758	1.00[EUR][1000 genomes]
rs73979025	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979028	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979045	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979046	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979047	0.81[AFR][1000 genomes]
rs73979048	1.00[EUR][1000 genomes]
rs73979049	1.00[EUR][1000 genomes]
rs73979056	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979057	1.00[EUR][1000 genomes]
rs73979063	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979079	1.00[EUR][1000 genomes]
rs73979080	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979088	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979096	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979097	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73981903	1.00[EUR][1000 genomes]
rs73981904	1.00[EUR][1000 genomes]
rs8079021	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1058863	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv543227	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv907727	chr17:16892265-16938582	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv962271	chr17:16912264-16922846	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16906800-16923400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr17:16915000-16923600	Weak transcription	HSMMtube	muscle
3	chr17:16917400-16923800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr17:16917400-16926200	Enhancers	Stomach Mucosa	stomach
5	chr17:16918000-16926200	Enhancers	Placenta	Placenta
6	chr17:16918600-16924200	Weak transcription	Osteobl	bone
7	chr17:16918800-16923200	Weak transcription	HSMM	muscle
8	chr17:16918800-16924200	Enhancers	Hela-S3	cervix
9	chr17:16918800-16924200	Weak transcription	K562	blood
10	chr17:16918800-16930800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr17:16919000-16922800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr17:16919000-16924200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr17:16919200-16923600	Weak transcription	Brain Anterior Caudate	brain
14	chr17:16919200-16924200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr17:16919200-16924200	Weak transcription	Small Intestine	intestine
16	chr17:16919800-16926200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr17:16920200-16923600	Enhancers	Placenta Amnion	Placenta Amnion
18	chr17:16920200-16926200	Enhancers	Pancreas	Pancrea
19	chr17:16920400-16923800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr17:16921000-16923800	Enhancers	Esophagus	oesophagus
21	chr17:16921000-16923800	Enhancers	NHEK	skin
22	chr17:16921000-16924200	Enhancers	Lung	lung
23	chr17:16921000-16924400	Enhancers	Fetal Intestine Small	intestine
24	chr17:16921000-16926200	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr17:16921200-16923400	Enhancers	Fetal Thymus	thymus
26	chr17:16921200-16924200	Enhancers	Fetal Intestine Large	intestine
27	chr17:16921200-16925400	Enhancers	HMEC	breast
28	chr17:16921400-16924800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr17:16921800-16924200	Enhancers	A549	lung
30	chr17:16922200-16923600	Enhancers	HepG2	liver
31	chr17:16922200-16924400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr17:16922400-16924200	Weak transcription	Colonic Mucosa	Colon
33	chr17:16922400-16925400	Weak transcription	Spleen	Spleen
34	chr17:16922400-16928000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr17:16922600-16924200	Weak transcription	Fetal Lung	lung
36	chr17:16922600-16924400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr17:16922600-16925200	Weak transcription	Gastric	stomach

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