Variant report

Variant	rs73980725
Chromosome Location	chr17:19801160-19801161
allele	A/C
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	POLR2A	chr17:19800633-19801494	U87	brain:	n/a	n/a
2	POLR2A	chr17:19801151-19801660	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr17:19799931-19805138	K562	blood:	n/a	n/a
4	POLR2A	chr17:19800354-19801678	Hela-S3	cervix:	n/a	n/a
5	USF2	chr17:19800438-19801800	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr17:19800720-19801406	HepG2	liver:	n/a	n/a
7	GATA3	chr17:19801074-19801744	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr17:19801054-19801504	GM12892	blood:	n/a	n/a
9	PBX3	chr17:19801160-19801768	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr17:19801063-19801317	GM12878	blood:	n/a	n/a
11	POLR2A	chr17:19800945-19801495	Hela-S3	cervix:	n/a	n/a
12	FOSL2	chr17:19801065-19801425	HepG2	liver:	n/a	chr17:19801184-19801193
13	GATA3	chr17:19801071-19801716	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr17:19800387-19801559	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr17:19801099-19801505	GM12878	blood:	n/a	n/a
16	POLR2A	chr17:19801067-19801467	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr17:19800639-19801494	U87	brain:	n/a	n/a
18	POLR2A	chr17:19801066-19801366	H1-hESC	embryonic stem cell:	n/a	n/a
19	GATA3	chr17:19801121-19801746	A549	lung:	n/a	n/a
20	POLR2A	chr17:19801093-19801391	K562	blood:	n/a	n/a
21	POLR2A	chr17:19800460-19801345	MCF-7	breast:	n/a	n/a
22	POLR2A	chr17:19801130-19801501	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr17:19800128-19801653	MCF10A-Er-Src	breast:	n/a	n/a
24	GTF2F1	chr17:19800323-19801545	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr17:19800145-19801337	GM12878	blood:	n/a	n/a
26	STAT3	chr17:19801111-19801668	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19769802..19772027-chr17:19799780..19804333,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270091	TF binding region
ENSG00000083290	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs56178618	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57853272	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58524683	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59395638	1.00[AMR][1000 genomes]
rs59704385	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7215558	0.81[AFR][1000 genomes]
rs7221750	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73980727	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73980759	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73980761	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73980764	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73980785	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73980787	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73980789	0.91[AFR][1000 genomes]
rs73980794	0.94[AFR][1000 genomes]
rs73984562	0.82[AFR][1000 genomes]
rs8064839	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8066256	0.88[AFR][1000 genomes]
rs8073950	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8082216	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv482398	chr17:19673458-19808039	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv518888	chr17:19789453-19804247	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19796400-19809800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:19798400-19804000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr17:19799200-19808400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:19799400-19803800	Weak transcription	Thymus	Thymus
5	chr17:19799400-19805000	Weak transcription	Fetal Intestine Large	intestine
6	chr17:19799600-19803800	Weak transcription	Primary T cells from cord blood	blood
7	chr17:19799800-19805200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr17:19799800-19806800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr17:19799800-19807000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr17:19800000-19801600	Enhancers	Fetal Heart	heart
11	chr17:19800000-19802200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr17:19800200-19801600	Enhancers	Colon Smooth Muscle	Colon
13	chr17:19800200-19802000	Enhancers	A549	lung
14	chr17:19800200-19802200	Flanking Active TSS	Hela-S3	cervix
15	chr17:19800200-19802200	Enhancers	HSMMtube	muscle
16	chr17:19800200-19804000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr17:19800400-19801200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr17:19800400-19801200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr17:19800400-19801200	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr17:19800400-19801400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr17:19800400-19801400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr17:19800400-19801400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr17:19800400-19801400	Enhancers	Adipose Nuclei	Adipose
24	chr17:19800400-19801400	Enhancers	Duodenum Mucosa	Duodenum
25	chr17:19800400-19801400	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr17:19800400-19801400	Enhancers	Fetal Muscle Leg	muscle
27	chr17:19800400-19801400	Enhancers	Lung	lung
28	chr17:19800400-19801400	Enhancers	Right Atrium	heart
29	chr17:19800400-19801400	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr17:19800400-19801400	Enhancers	Stomach Smooth Muscle	stomach
31	chr17:19800400-19801400	Enhancers	HMEC	breast
32	chr17:19800400-19801400	Enhancers	NHLF	lung
33	chr17:19800400-19801800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr17:19800400-19802000	Enhancers	NHEK	skin
35	chr17:19800400-19802200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr17:19800400-19802200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr17:19800400-19802400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr17:19800400-19802400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr17:19800600-19801200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr17:19800600-19801400	Enhancers	Colonic Mucosa	Colon
41	chr17:19800600-19801400	Enhancers	Gastric	stomach
42	chr17:19800600-19801400	Enhancers	Right Ventricle	heart
43	chr17:19800600-19801600	Enhancers	Osteobl	bone
44	chr17:19800600-19802200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr17:19800600-19802200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr17:19800600-19802200	Enhancers	HSMM	muscle
47	chr17:19800600-19802200	Enhancers	NHDF-Ad	bronchial
48	chr17:19800600-19802800	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr17:19800600-19802800	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr17:19800600-19803000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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