Variant report

Variant	rs3744449
Chromosome Location	chr17:59473880-59473881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:59468390-59479830	ProgFib	skin:	n/a	n/a
2	TEAD4	chr17:59473743-59474466	A549	lung:	n/a	n/a
3	SUZ12	chr17:59472440-59474557	H1-hESC	embryonic stem cell:	n/a	n/a
4	SUZ12	chr17:59473583-59483306	NT2-D1	testis:	n/a	n/a
5	CTBP2	chr17:59473490-59474626	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAZ	chr17:59472821-59478277	IMR90	lung:	n/a	chr17:59474298-59474308 chr17:59475824-59475831 chr17:59474536-59474546 chr17:59474205-59474214
7	POLR2A	chr17:59473262-59482475	IMR90	lung:	n/a	n/a
8	POLR2A	chr17:59473844-59474034	HepG2	liver:	n/a	n/a
9	MXI1	chr17:59473244-59478459	IMR90	lung:	n/a	n/a
10	POLR2A	chr17:59468021-59474379	Hela-S3	cervix:	n/a	n/a

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:59473143..59474967-chr17:59892962..59895901,2	MCF-7	breast:
2	chr17:59473327..59475095-chr20:54154216..54156419,2	MCF-7	breast:
3	chr17:59469164..59471645-chr17:59472250..59474321,2	K562	blood:
4	chr17:59415713..59496229-chr20:49401322..49431802,760	MCF-7	breast:
5	chr17:57914760..57924876-chr17:59472133..59480361,28	MCF-7	breast:
6	chr13:27998498..28000726-chr17:59473346..59475329,2	MCF-7	breast:
7	chr17:59468937..59480240-chr20:49340039..49356868,49	MCF-7	breast:
8	chr17:59468469..59482635-chr20:45977748..45992950,51	MCF-7	breast:
9	chr17:56706858..56710627-chr17:59472052..59479583,11	MCF-7	breast:
10	chr17:59473100..59476327-chr17:59937643..59941414,3	MCF-7	breast:
11	chr17:37355309..37357444-chr17:59472503..59475365,2	MCF-7	breast:
12	chr11:61193958..61196849-chr17:59473654..59475823,2	MCF-7	breast:
13	chr12:120728045..120729780-chr17:59472665..59474429,2	MCF-7	breast:
14	chr17:59473508..59476352-chr2:219187700..219189664,2	MCF-7	breast:
15	chr17:59473116..59475662-chr20:49369378..49372060,2	MCF-7	breast:
16	chr17:59471714..59474637-chr20:45985553..45987667,2	MCF-7	breast:
17	chr17:59470525..59474011-chr17:59486288..59490375,89	MCF-7	breast:
18	chr17:56728030..56730756-chr17:59473756..59475323,2	MCF-7	breast:
19	chr17:59468167..59483990-chr20:49341590..49352501,35	MCF-7	breast:
20	chr1:112530336..112534122-chr17:59473481..59479325,11	MCF-7	breast:
21	chr17:59472839..59476239-chr3:161133074..161135554,3	MCF-7	breast:
22	chr17:59473769..59475207-chr20:49410926..49411979,4	MCF-7	breast:
23	chr17:59473726..59474625-chr17:59486735..59487548,2	MCF-7	breast:
24	chr17:59473576..59476219-chr7:75934153..75935761,2	MCF-7	breast:
25	chr17:59447417..59500105-chr20:49391742..49424382,639	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NACA2-2	chr17:59473370-59474207	XLOC_012542

No data

Variant related genes	Relation type
ENSG00000267280	TF binding region
TBX2	TF binding region
ENSG00000136492	Chromatin interaction
ENSG00000149532	Chromatin interaction
ENSG00000108298	Chromatin interaction
ENSG00000273451	Chromatin interaction
ENSG00000231437	Chromatin interaction
ENSG00000256591	Chromatin interaction
ENSG00000127838	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000231119	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000124243	Chromatin interaction
ENSG00000171385	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000122034	Chromatin interaction
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1076393	0.96[EUR][1000 genomes]
rs1132179	0.88[EUR][1000 genomes]
rs12451524	0.96[EUR][1000 genomes]
rs2286524	1.00[EUR][1000 genomes]
rs3760369	1.00[EUR][1000 genomes]
rs4455026	0.95[EUR][1000 genomes]
rs59051236	0.90[EUR][1000 genomes]
rs7208889	0.96[EUR][1000 genomes]
rs7214900	0.85[EUR][1000 genomes]
rs729782	0.95[EUR][1000 genomes]
rs740753	0.90[EUR][1000 genomes]
rs740754	0.90[EUR][1000 genomes]
rs8066348	0.96[EUR][1000 genomes]
rs8075606	0.96[EUR][1000 genomes]
rs8078820	1.00[EUR][1000 genomes]
rs8080990	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	esv3374888	chr17:59473395-59475943	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59464000-59474000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr17:59467400-59474000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr17:59470800-59476000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr17:59471400-59474000	Bivalent Enhancer	Fetal Muscle Leg	muscle
5	chr17:59471800-59475400	Weak transcription	A549	lung
6	chr17:59472000-59474000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr17:59472200-59474000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr17:59472200-59475000	Weak transcription	HSMM	muscle
9	chr17:59472400-59474000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr17:59472400-59474000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr17:59472400-59474200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
12	chr17:59472600-59474000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
13	chr17:59472600-59474600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr17:59472600-59475800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr17:59472800-59474000	Weak transcription	NHDF-Ad	bronchial
16	chr17:59472800-59474200	Bivalent/Poised TSS	Fetal Stomach	stomach
17	chr17:59472800-59475400	Weak transcription	Hela-S3	cervix
18	chr17:59473000-59474000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr17:59473000-59474000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
20	chr17:59473000-59474000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
21	chr17:59473000-59474000	Active TSS	NHLF	lung
22	chr17:59473000-59476000	Bivalent/Poised TSS	Fetal Lung	lung
23	chr17:59473200-59474200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr17:59473200-59474600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr17:59473200-59475000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
26	chr17:59473200-59475000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
27	chr17:59473200-59475200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
28	chr17:59473200-59475200	Active TSS	Ovary	ovary
29	chr17:59473200-59475400	Bivalent Enhancer	Fetal Heart	heart
30	chr17:59473400-59474000	Bivalent/Poised TSS	Esophagus	oesophagus
31	chr17:59473400-59474000	Bivalent/Poised TSS	Lung	lung
32	chr17:59473400-59474000	Enhancers	Pancreas	Pancrea
33	chr17:59473400-59474000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
34	chr17:59473400-59474200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr17:59473400-59474200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
36	chr17:59473400-59474400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
37	chr17:59473400-59475000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
38	chr17:59473400-59475000	Bivalent/Poised TSS	Colonic Mucosa	Colon
39	chr17:59473400-59475200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
40	chr17:59473400-59476200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr17:59473400-59476200	Bivalent/Poised TSS	Psoas Muscle	Psoas
42	chr17:59473400-59476400	Bivalent Enhancer	Brain Germinal Matrix	brain
43	chr17:59473400-59477000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
44	chr17:59473400-59479800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
45	chr17:59473600-59474000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
46	chr17:59473600-59474000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr17:59473600-59474000	Bivalent Enhancer	Fetal Intestine Large	intestine
48	chr17:59473600-59474000	Bivalent Enhancer	Fetal Intestine Small	intestine
49	chr17:59473600-59474000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
50	chr17:59473600-59474400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain

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