Variant report

Variant	rs3809858
Chromosome Location	chr17:45267212-45267213
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	TBL1XR1	chr17:45266037-45267227	K562	blood:	n/a	n/a
2	POLR2A	chr17:45266115-45267352	U87	brain:	n/a	n/a
3	POLR2A	chr17:45266090-45267262	K562	blood:	n/a	n/a
4	PML	chr17:45265840-45267289	GM12878	blood:	n/a	chr17:45266841-45266849
5	ARID3A	chr17:45266342-45267543	K562	blood:	n/a	n/a
6	CEBPB	chr17:45266154-45267265	Hela-S3	cervix:	n/a	n/a
7	HCFC1	chr17:45265488-45267486	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr17:45265465-45267232	SK-N-SH	brain:	n/a	n/a
9	TBP	chr17:45265561-45267241	Hela-S3	cervix:	n/a	n/a
10	TAL1	chr17:45266343-45267306	K562	blood:	n/a	n/a
11	SP1	chr17:45266129-45267351	A549	lung:	n/a	chr17:45266932-45266942 chr17:45266876-45266886 chr17:45266876-45266886
12	POLR2A	chr17:45266021-45267276	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr17:45265550-45267318	SK-N-MC	brain:	n/a	n/a
14	HA-E2F1	chr17:45266089-45267233	MCF-7	breast:	n/a	chr17:45266399-45266411
15	NR2F2	chr17:45265332-45267743	K562	blood:	n/a	n/a
16	TEAD4	chr17:45266237-45267237	K562	blood:	n/a	n/a
17	EP300	chr17:45266166-45267590	K562	blood:	n/a	chr17:45266426-45266442
18	POLR2A	chr17:45265572-45267221	GM12891	blood:	n/a	n/a
19	TBL1XR1	chr17:45266245-45267250	GM12878	blood:	n/a	n/a
20	POLR2A	chr17:45265705-45267214	Raji	blood:	n/a	n/a
21	IRF1	chr17:45266120-45268008	K562	blood:	n/a	chr17:45267928-45267938 chr17:45267398-45267412 chr17:45266840-45266854 chr17:45267922-45267939 chr17:45267928-45267942 chr17:45267924-45267938 chr17:45266838-45266852 chr17:45267401-45267418 chr17:45267927-45267939
22	POLR2A	chr17:45266216-45267251	U87	brain:	n/a	n/a
23	JUN	chr17:45265467-45268646	K562	blood:	n/a	chr17:45266621-45266629 chr17:45265547-45265555 chr17:45266398-45266407 chr17:45265547-45265554
24	TEAD4	chr17:45266698-45267301	K562	blood:	n/a	n/a
25	POLR2A	chr17:45266330-45267251	SK-N-MC	brain:	n/a	n/a
26	POLR2A	chr17:45265740-45267273	Hela-S3	cervix:	n/a	n/a
27	ZMIZ1	chr17:45266350-45267257	K562	blood:	n/a	n/a
28	HEY1	chr17:45265609-45267222	K562	blood:	n/a	chr17:45266587-45266602
29	POLR2A	chr17:45266065-45267228	HUVEC	blood vessel:	n/a	n/a
30	GATA3	chr17:45267124-45267535	SH-SY5Y	brain:	n/a	chr17:45267318-45267325 chr17:45267318-45267328 chr17:45267308-45267324 chr17:45267308-45267324
31	KAP1	chr17:45266149-45267240	HEK293	kidney:	n/a	chr17:45266841-45266849
32	MYBL2	chr17:45265742-45267272	HepG2	liver:	n/a	n/a
33	POLR2A	chr17:45265722-45267217	Hela-S3	cervix:	n/a	n/a
34	TAF1	chr17:45265931-45267265	A549	lung:	n/a	n/a
35	TBP	chr17:45265585-45267220	K562	blood:	n/a	n/a
36	POLR2A	chr17:45265426-45267360	IMR90	lung:	n/a	n/a
37	JUND	chr17:45265580-45267231	K562	blood:	n/a	chr17:45266621-45266629 chr17:45266398-45266407
38	TCF12	chr17:45266076-45267228	ECC-1	luminal epithelium:	n/a	n/a
39	TBL1XR1	chr17:45265708-45267228	K562	blood:	n/a	n/a
40	POLR2A	chr17:45266115-45267385	U87	brain:	n/a	n/a
41	MAX	chr17:45265502-45267382	A549	lung:	n/a	n/a
42	RFX5	chr17:45265606-45267308	Hela-S3	cervix:	n/a	n/a
43	SIX5	chr17:45266060-45267269	A549	lung:	n/a	n/a
44	IRF1	chr17:45266339-45267237	K562	blood:	n/a	chr17:45266840-45266854 chr17:45266838-45266852
45	CEBPB	chr17:45266161-45267214	K562	blood:	n/a	n/a
46	MAX	chr17:45266082-45267222	ECC-1	luminal epithelium:	n/a	n/a
47	MTA3	chr17:45265496-45267302	GM12878	blood:	n/a	n/a
48	GATA1	chr17:45266205-45268128	PBDE	blood:	n/a	chr17:45267318-45267325 chr17:45267318-45267328 chr17:45267308-45267324 chr17:45267308-45267324 chr17:45266480-45266488
49	PML	chr17:45266184-45267300	K562	blood:	n/a	chr17:45266841-45266849
50	NFIC	chr17:45266091-45267305	HepG2	liver:	n/a	chr17:45266470-45266487

No.	Distal block	Cell Line	Cell type
1	chr17:45256968..45259015-chr17:45265544..45267226,2	MCF-7	breast:
2	chr17:45264972..45267284-chr17:45403808..45405423,2	K562	blood:
3	chr17:45247336..45250133-chr17:45265157..45267526,3	MCF-7	breast:
4	chr17:45264884..45268790-chr17:45285196..45288860,4	K562	blood:
5	chr17:45264174..45269379-chr17:45283146..45288200,6	K562	blood:

Variant related genes	Relation type
CDC27	TF binding region
ENSG00000178852	Chromatin interaction
ENSG00000198336	Chromatin interaction
ENSG00000004897	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11079760	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11570468	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11570511	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11570546	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs12601027	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs16941622	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16941662	0.92[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3785874	0.92[CEU][hapmap];0.83[CHB][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs66945411	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67305320	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67861319	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45265200-45267400	Active TSS	Muscle Satellite Cultured Cells	--
2	chr17:45265200-45267400	Active TSS	Brain Germinal Matrix	brain
3	chr17:45265200-45267400	Active TSS	Fetal Brain Female	brain
4	chr17:45265400-45267400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr17:45265400-45267400	Active TSS	Fetal Intestine Small	intestine
6	chr17:45265600-45267400	Active TSS	Osteobl	bone
7	chr17:45266000-45267400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr17:45266000-45267600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr17:45266600-45267400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr17:45266600-45267400	Active TSS	Primary hematopoietic stem cells	blood
11	chr17:45266600-45267400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr17:45266600-45267400	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr17:45266600-45267400	Active TSS	NH-A	brain
14	chr17:45266800-45267400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr17:45266800-45267400	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr17:45266800-45267400	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr17:45266800-45267400	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr17:45266800-45267400	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr17:45266800-45267400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr17:45266800-45267400	Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr17:45266800-45267400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr17:45266800-45267400	Active TSS	Adipose Nuclei	Adipose
23	chr17:45266800-45267400	Active TSS	Brain Anterior Caudate	brain
24	chr17:45266800-45267400	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr17:45266800-45267400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
26	chr17:45266800-45267400	Active TSS	Fetal Intestine Large	intestine
27	chr17:45266800-45267400	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr17:45266800-45267400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr17:45266800-45267400	Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr17:45266800-45267400	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr17:45266800-45267400	Active TSS	Stomach Smooth Muscle	stomach
32	chr17:45266800-45268200	Weak transcription	Lung	lung
33	chr17:45266800-45270200	Weak transcription	Small Intestine	intestine
34	chr17:45266800-45277800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr17:45267000-45267400	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr17:45267000-45267400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr17:45267000-45267400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr17:45267000-45267400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr17:45267000-45267400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr17:45267000-45267400	Flanking Active TSS	Dnd41	blood
41	chr17:45267000-45267400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr17:45267200-45267400	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr17:45267200-45267400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr17:45267200-45267400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr17:45267200-45267400	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr17:45267200-45267400	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr17:45267200-45267400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr17:45267200-45267400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr17:45267200-45267400	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr17:45267200-45267400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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