Variant report

Variant	rs58804619
Chromosome Location	chr17:18090654-18090655
allele	C/G
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	CHD1	chr17:18085856-18091134	IMR90	lung:	n/a	n/a
2	MXI1	chr17:18085581-18092228	SK-N-SH	brain:	n/a	chr17:18086672-18086687 chr17:18088362-18088377
3	POLR2A	chr17:18090411-18090995	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr17:18090491-18090890	SH-SY5Y	brain:	n/a	n/a
5	EP300	chr17:18087589-18092262	SK-N-SH	brain:	n/a	chr17:18089998-18090012
6	WRNIP1	chr17:18087774-18091201	GM12878	blood:	n/a	n/a
7	POLR2A	chr17:18090531-18090978	HepG2	liver:	n/a	n/a
8	POLR2A	chr17:18089745-18090829	U87	brain:	n/a	n/a
9	KAP1	chr17:18087725-18091513	HEK293	kidney:	n/a	chr17:18091056-18091064
10	TCF12	chr17:18090282-18091198	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr17:18090521-18090917	HepG2	liver:	n/a	n/a
12	GATA2	chr17:18090537-18091829	SH-SY5Y	brain:	n/a	n/a
13	PBX3	chr17:18090445-18091121	SK-N-SH	brain:	n/a	n/a
14	RUNX3	chr17:18090459-18090745	GM12878	blood:	n/a	n/a
15	GATA3	chr17:18090355-18092100	SK-N-SH	brain:	n/a	n/a
16	NFIC	chr17:18090468-18092116	SK-N-SH	brain:	n/a	n/a
17	PBX3	chr17:18090416-18091082	SK-N-SH	brain:	n/a	n/a
18	RAD21	chr17:18090453-18090893	SK-N-SH_RA	brain:	n/a	n/a
19	YY1	chr17:18090331-18090808	SK-N-SH_RA	brain:	n/a	n/a
20	POLR2A	chr17:18090614-18091050	HepG2	liver:	n/a	n/a
21	MXI1	chr17:18086003-18091020	IMR90	lung:	n/a	chr17:18086672-18086687 chr17:18088362-18088377
22	YY1	chr17:18090422-18091105	SK-N-SH_RA	brain:	n/a	n/a
23	EP300	chr17:18090411-18091040	SK-N-SH_RA	brain:	n/a	n/a
24	TCF12	chr17:18089654-18092249	SK-N-SH	brain:	n/a	n/a
25	EP300	chr17:18090320-18091075	SK-N-SH_RA	brain:	n/a	n/a
26	SMC3	chr17:18090483-18090671	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:18088851..18092330-chr17:18106978..18109728,3	K562	blood:
2	chr17:18081720..18083275-chr17:18090040..18091651,2	MCF-7	breast:
3	chr17:18089295..18091873-chr17:18217649..18220179,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266677	TF binding region
ENSG00000177302	Chromatin interaction
ENSG00000176994	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1064629	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12449609	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12450483	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2056841	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2072652	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2072653	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2075659	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2242595	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2272571	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4925145	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925147	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57186648	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59179192	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72827432	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8068517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv907770	chr17:18003845-18098018	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv907771	chr17:18013560-18098018	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv907772	chr17:18030524-18098018	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv510702	chr17:18037676-18116801	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18087800-18091200	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr17:18087800-18092000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr17:18087800-18092200	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr17:18088000-18090800	Flanking Active TSS	Liver	Liver
5	chr17:18088000-18091200	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
6	chr17:18088000-18091800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr17:18088000-18092000	Flanking Active TSS	HUVEC	blood vessel
8	chr17:18088000-18093000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr17:18088200-18090800	Flanking Active TSS	Fetal Brain Female	brain
10	chr17:18088200-18091000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
11	chr17:18088200-18091000	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
12	chr17:18088200-18091200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr17:18088200-18091200	Flanking Active TSS	Fetal Brain Male	brain
14	chr17:18088200-18091400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr17:18088200-18091400	Transcr. at gene 5' and 3'	Thymus	Thymus
16	chr17:18088200-18092000	Flanking Active TSS	Brain Germinal Matrix	brain
17	chr17:18088200-18092000	Flanking Active TSS	NH-A	brain
18	chr17:18088400-18091200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr17:18088600-18091000	Flanking Active TSS	Brain Substantia Nigra	brain
20	chr17:18088800-18091000	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr17:18088800-18091000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
22	chr17:18088800-18091000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
23	chr17:18088800-18091000	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
24	chr17:18088800-18091000	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
25	chr17:18088800-18091200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr17:18088800-18091200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr17:18088800-18091200	Transcr. at gene 5' and 3'	A549	lung
28	chr17:18088800-18091400	Flanking Active TSS	Brain Anterior Caudate	brain
29	chr17:18088800-18091400	Flanking Active TSS	Psoas Muscle	Psoas
30	chr17:18088800-18092000	Flanking Active TSS	Brain Hippocampus Middle	brain
31	chr17:18088800-18092000	Transcr. at gene 5' and 3'	NHEK	skin
32	chr17:18088800-18092200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr17:18088800-18092200	Flanking Active TSS	Osteobl	bone
34	chr17:18089000-18091000	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
35	chr17:18089000-18091200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
36	chr17:18089000-18091200	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
37	chr17:18089000-18091200	Flanking Active TSS	Fetal Heart	heart
38	chr17:18089000-18091400	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr17:18089000-18091600	Transcr. at gene 5' and 3'	K562	blood
40	chr17:18089000-18091800	Flanking Active TSS	Colon Smooth Muscle	Colon
41	chr17:18089000-18091800	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
42	chr17:18089000-18092000	Flanking Active TSS	Brain Angular Gyrus	brain
43	chr17:18089000-18092000	Flanking Active TSS	Rectal Smooth Muscle	rectum
44	chr17:18089000-18095400	Enhancers	Small Intestine	intestine
45	chr17:18089200-18091000	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
46	chr17:18089200-18091000	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
47	chr17:18089200-18091000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr17:18089200-18091200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr17:18089200-18091200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr17:18089200-18091600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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