Variant report

Variant	rs1057987
Chromosome Location	chr17:59485555-59485556
allele	A/C/G/T
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	GATA3	chr17:59484270-59486381	MCF-7	breast:	n/a	n/a
2	SUZ12	chr17:59484289-59486441	H1-hESC	embryonic stem cell:	n/a	n/a
3	TEAD4	chr17:59484276-59495088	A549	lung:	n/a	n/a
4	RAD21	chr17:59483140-59491480	MCF-7	breast:	n/a	chr17:59488343-59488353 chr17:59488338-59488357 chr17:59491210-59491220 chr17:59488536-59488550 chr17:59488875-59488884 chr17:59488341-59488354 chr17:59487989-59487999 chr17:59488343-59488355
5	POLR2A	chr17:59484175-59490331	ProgFib	skin:	n/a	n/a
6	MAX	chr17:59484138-59500997	MCF-7	breast:	n/a	chr17:59495541-59495552 chr17:59492978-59492987 chr17:59491213-59491223 chr17:59491485-59491495 chr17:59495570-59495581 chr17:59488910-59488926
7	POLR2A	chr17:59485546-59491030	SK-N-SH	brain:	n/a	n/a
8	HDAC2	chr17:59482687-59495676	MCF-7	breast:	n/a	chr17:59487075-59487094 chr17:59495598-59495612 chr17:59495596-59495610 chr17:59495599-59495613 chr17:59495595-59495609 chr17:59494256-59494265 chr17:59492574-59492588
9	CTBP2	chr17:59485485-59487053	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:7052718..7054470-chr17:59484968..59487840,2	MCF-7	breast:
2	chr15:69580447..69583184-chr17:59484403..59487018,2	MCF-7	breast:
3	chr17:57057316..57060250-chr17:59483585..59485883,2	MCF-7	breast:
4	chr17:59415713..59496229-chr20:49401322..49431802,760	MCF-7	breast:
5	chr17:59483854..59486067-chr17:59939146..59941681,2	MCF-7	breast:
6	chr17:59485117..59489801-chr22:29195073..29197990,4	MCF-7	breast:
7	chr17:59485530..59487637-chr20:52824425..52826103,2	MCF-7	breast:
8	chr17:56734979..56738872-chr17:59484133..59487824,5	MCF-7	breast:
9	chr17:59485283..59487491-chr8:96036990..96038836,2	MCF-7	breast:
10	chr17:57917727..57920110-chr17:59485356..59487364,3	MCF-7	breast:
11	chr17:58156445..58158243-chr17:59484791..59486800,2	MCF-7	breast:
12	chr17:59485092..59487967-chr20:49409770..49412327,54	MCF-7	breast:
13	chr17:59484193..59487326-chr20:49346674..49350081,5	MCF-7	breast:
14	chr17:59485426..59486139-chr20:49411436..49412006,2	MCF-7	breast:
15	chr17:59482922..59485740-chr20:52327701..52330610,2	MCF-7	breast:
16	chr17:56707801..56710950-chr17:59485321..59490857,5	MCF-7	breast:
17	chr17:59484671..59491871-chr20:55837745..55844407,10	MCF-7	breast:
18	chr1:112529769..112535605-chr17:59484879..59491283,15	MCF-7	breast:
19	chr14:35022483..35025018-chr17:59483690..59486077,2	MCF-7	breast:
20	chr17:59485481..59487209-chr20:39766303..39768630,2	MCF-7	breast:
21	chr17:59076528..59085339-chr17:59484802..59491356,15	MCF-7	breast:
22	chr17:59484738..59486572-chr7:6745021..6746847,2	MCF-7	breast:
23	chr1:112571478..112575013-chr17:59482604..59485824,3	MCF-7	breast:
24	chr12:76425879..76428057-chr17:59483669..59485825,2	MCF-7	breast:
25	chr16:89762693..89764669-chr17:59483931..59485928,2	MCF-7	breast:
26	chr12:123872784..123874602-chr17:59484787..59486930,2	MCF-7	breast:
27	chr17:57913418..57928047-chr17:59480816..59492160,26	MCF-7	breast:
28	chr17:59447417..59500105-chr20:49391742..49424382,639	MCF-7	breast:

Variant related genes	Relation type
TBX2	TF binding region
C17orf82	TF binding region
ENSG00000139289	Chromatin interaction
ENSG00000272173	Chromatin interaction
ENSG00000226648	Chromatin interaction
ENSG00000257839	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000267416	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000261634	Chromatin interaction
ENSG00000164631	Chromatin interaction
ENSG00000171385	Chromatin interaction
ENSG00000124181	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000238923	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000111678	Chromatin interaction
ENSG00000124243	Chromatin interaction
ENSG00000226471	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000100219	Chromatin interaction
ENSG00000231437	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000156170	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000141376	Chromatin interaction
ENSG00000101132	Chromatin interaction
ENSG00000136492	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1000423	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1058004	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10853031	0.87[ASN][1000 genomes]
rs11868532	0.91[ASN][1000 genomes]
rs11871637	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12952625	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2240736	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2270114	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2286526	0.91[EUR][1000 genomes]
rs34446110	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62071306	0.82[ASN][1000 genomes]
rs7215775	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs729781	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8068318	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8073698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8074151	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8078036	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9891115	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9905140	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065939	chr17:59283350-59517730	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	331 gene(s)	inside rSNPs	diseases
2	nsv833505	chr17:59323466-59518007	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	326 gene(s)	inside rSNPs	diseases
3	nsv833506	chr17:59362377-59562984	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
4	nsv518130	chr17:59456589-59491281	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	265 gene(s)	inside rSNPs	diseases
5	esv1796927	chr17:59460119-59495319	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	270 gene(s)	inside rSNPs	diseases
6	nsv908663	chr17:59464069-59521310	Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	278 gene(s)	inside rSNPs	diseases
7	nsv908664	chr17:59465697-59491030	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	261 gene(s)	inside rSNPs	diseases
8	nsv908665	chr17:59470193-59494574	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
9	nsv908666	chr17:59470842-59489822	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	253 gene(s)	inside rSNPs	diseases
10	nsv908667	chr17:59471151-59491030	Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	256 gene(s)	inside rSNPs	diseases
11	nsv908668	chr17:59471151-59494574	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	263 gene(s)	inside rSNPs	diseases
12	nsv908669	chr17:59471372-59491030	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	255 gene(s)	inside rSNPs	diseases
13	nsv908670	chr17:59471372-59494574	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	262 gene(s)	inside rSNPs	diseases
14	nsv908671	chr17:59475888-59494574	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	255 gene(s)	inside rSNPs	diseases
15	nsv908672	chr17:59476062-59494574	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	255 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59478000-59488200	Transcr. at gene 5' and 3'	NHLF	lung
2	chr17:59478200-59487600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr17:59478200-59487800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr17:59478600-59486400	Weak transcription	A549	lung
5	chr17:59479000-59486600	Weak transcription	HSMMtube	muscle
6	chr17:59479400-59487200	Weak transcription	Hela-S3	cervix
7	chr17:59480200-59486400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr17:59480400-59486000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr17:59480400-59486200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr17:59480400-59486400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr17:59480400-59488000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr17:59481600-59485800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr17:59482200-59486400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr17:59482400-59486200	Weak transcription	Aorta	Aorta
15	chr17:59482800-59486000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr17:59483000-59486200	Weak transcription	Pancreas	Pancrea
17	chr17:59483200-59486600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr17:59483400-59486200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr17:59483400-59486400	Weak transcription	Right Atrium	heart
20	chr17:59483800-59485600	Enhancers	HepG2	liver
21	chr17:59483800-59485800	Strong transcription	Osteobl	bone
22	chr17:59484000-59486000	Bivalent Enhancer	Fetal Stomach	stomach
23	chr17:59484000-59486600	Weak transcription	Ovary	ovary
24	chr17:59484200-59486000	Bivalent Enhancer	Adipose Nuclei	Adipose
25	chr17:59484400-59485600	Enhancers	Psoas Muscle	Psoas
26	chr17:59484400-59487000	Bivalent Enhancer	Spleen	Spleen
27	chr17:59484600-59486200	Enhancers	NHDF-Ad	bronchial
28	chr17:59484600-59486600	Bivalent Enhancer	Fetal Intestine Large	intestine
29	chr17:59484600-59486600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr17:59484600-59487200	Enhancers	Liver	Liver
31	chr17:59484800-59485600	Bivalent/Poised TSS	Colonic Mucosa	Colon
32	chr17:59484800-59485800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr17:59485000-59486400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
34	chr17:59485000-59486400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr17:59485000-59486400	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
36	chr17:59485000-59486600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
37	chr17:59485000-59486600	Enhancers	Gastric	stomach
38	chr17:59485000-59486600	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
39	chr17:59485000-59487800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
40	chr17:59485200-59485800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
41	chr17:59485200-59486000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
42	chr17:59485200-59486000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
43	chr17:59485200-59486000	Bivalent Enhancer	Fetal Muscle Leg	muscle
44	chr17:59485200-59486200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr17:59485200-59486200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
46	chr17:59485200-59486600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
47	chr17:59485200-59486600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
48	chr17:59485200-59486600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
49	chr17:59485200-59486600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
50	chr17:59485200-59488000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell

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