Variant report

Variant	rs9568489
Chromosome Location	chr13:51467569-51467570
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	MTA3	chr13:51467178-51468170	GM12878	blood:	n/a	n/a
2	MAZ	chr13:51467313-51468079	GM12878	blood:	n/a	n/a
3	YY1	chr13:51467372-51468065	SK-N-SH_RA	brain:	n/a	chr13:51467903-51467922
4	POLR2A	chr13:51467239-51468115	GM12892	blood:	n/a	n/a
5	NFIC	chr13:51467548-51468204	GM12878	blood:	n/a	n/a
6	EP300	chr13:51467335-51467964	SK-N-SH	brain:	n/a	chr13:51467427-51467437 chr13:51467850-51467864
7	TAF1	chr13:51467561-51468102	GM12878	blood:	n/a	n/a
8	POLR2A	chr13:51466272-51468206	GM12892	blood:	n/a	n/a
9	PBX3	chr13:51467300-51467805	SK-N-SH	brain:	n/a	n/a
10	FOXM1	chr13:51467506-51468200	GM12878	blood:	n/a	n/a
11	MAX	chr13:51467385-51468660	NB4	blood:	n/a	n/a
12	PBX3	chr13:51467213-51467875	SK-N-SH	brain:	n/a	n/a
13	STAT3	chr13:51467200-51468089	GM12878	blood:	n/a	chr13:51468019-51468026 chr13:51467848-51467859
14	TBP	chr13:51467304-51468135	GM12878	blood:	n/a	n/a
15	GATA3	chr13:51467269-51468050	SH-SY5Y	brain:	n/a	chr13:51467784-51467793
16	CHD1	chr13:51467312-51468058	GM12878	blood:	n/a	n/a
17	GATA3	chr13:51467196-51468056	SK-N-SH	brain:	n/a	chr13:51467784-51467793
18	GATA3	chr13:51467230-51468046	SK-N-SH	brain:	n/a	chr13:51467784-51467793
19	POLR2A	chr13:51465521-51468914	GM12891	blood:	n/a	n/a
20	WRNIP1	chr13:51467515-51467572	GM12878	blood:	n/a	n/a
21	TCF12	chr13:51467219-51468084	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr13:51467368-51467581	SK-N-SH	brain:	n/a	n/a
23	BHLHE40	chr13:51467550-51468123	GM12878	blood:	n/a	n/a
24	ZNF384	chr13:51466301-51468162	GM12878	blood:	n/a	n/a
25	EP300	chr13:51467342-51468051	SK-N-SH_RA	brain:	n/a	chr13:51467427-51467437 chr13:51467850-51467864
26	POLR2A	chr13:51467351-51468490	HL-60	blood:	n/a	n/a
27	ATF2	chr13:51467449-51468203	GM12878	blood:	n/a	n/a
28	EP300	chr13:51467344-51468085	GM12878	blood:	n/a	chr13:51467427-51467437 chr13:51467850-51467864
29	POLR2A	chr13:51466288-51468163	GM12878	blood:	n/a	n/a
30	RUNX3	chr13:51467279-51468175	GM12878	blood:	n/a	n/a
31	MYC	chr13:51467396-51468443	NB4	blood:	n/a	n/a
32	GATA2	chr13:51467323-51467887	SH-SY5Y	brain:	n/a	chr13:51467784-51467793
33	EP300	chr13:51466210-51468760	SK-N-SH	brain:	n/a	chr13:51466712-51466726 chr13:51467427-51467437 chr13:51466668-51466677 chr13:51467057-51467071 chr13:51466667-51466681 chr13:51467051-51467065 chr13:51467850-51467864 chr13:51467053-51467067
34	IKZF1	chr13:51467403-51468034	GM12878	blood:	n/a	n/a
35	EP300	chr13:51467335-51468032	SK-N-SH_RA	brain:	n/a	chr13:51467427-51467437 chr13:51467850-51467864
36	NFIC	chr13:51467495-51468196	GM12878	blood:	n/a	n/a
37	BCLAF1	chr13:51467397-51468142	GM12878	blood:	n/a	chr13:51467850-51467859
38	MXI1	chr13:51467398-51468088	GM12878	blood:	n/a	n/a
39	TCF12	chr13:51467155-51468170	SK-N-SH	brain:	n/a	n/a
40	YY1	chr13:51467397-51467900	SK-N-SH_RA	brain:	n/a	n/a
41	POLR2A	chr13:51467282-51468111	SK-N-MC	brain:	n/a	n/a
42	POLR2A	chr13:51467342-51467884	SK-N-SH	brain:	n/a	n/a
43	MAX	chr13:51467233-51468075	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RNASEH2B-AS1	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs73186349	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs73186350	0.90[EUR][1000 genomes]
rs73186351	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73186353	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73186356	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73186357	0.89[AFR][1000 genomes]
rs73186363	0.85[ASN][1000 genomes]
rs9316510	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9316511	0.85[ASN][1000 genomes]
rs9526702	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9563009	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568485	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9568487	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv900077	chr13:51446114-51514831	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv900078	chr13:51454896-51478716	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51465600-51468400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr13:51465600-51474600	Weak transcription	Aorta	Aorta
3	chr13:51465800-51468400	Flanking Active TSS	Fetal Thymus	thymus
4	chr13:51466000-51467600	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr13:51466000-51468000	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr13:51466000-51469000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr13:51466000-51469000	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr13:51466000-51469200	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr13:51466200-51467600	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr13:51466200-51468000	Flanking Active TSS	Primary T cells from cord blood	blood
11	chr13:51466200-51468400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr13:51466200-51468800	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr13:51466400-51467800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr13:51466400-51468200	Enhancers	HSMM	muscle
15	chr13:51466400-51468400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr13:51466400-51468400	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr13:51466400-51468800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr13:51466600-51467600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr13:51466600-51467800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
20	chr13:51466600-51468200	Active TSS	Thymus	Thymus
21	chr13:51466600-51471000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr13:51466800-51467800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr13:51466800-51467800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
24	chr13:51466800-51467800	Active TSS	NHDF-Ad	bronchial
25	chr13:51466800-51468000	Enhancers	Muscle Satellite Cultured Cells	--
26	chr13:51467000-51468800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr13:51467000-51469000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr13:51467200-51467600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr13:51467200-51467600	Flanking Active TSS	Fetal Kidney	kidney
30	chr13:51467200-51467800	Active TSS	Primary T cells fromperipheralblood	blood
31	chr13:51467200-51467800	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr13:51467200-51467800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr13:51467200-51467800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr13:51467200-51467800	Active TSS	Stomach Smooth Muscle	stomach
35	chr13:51467200-51468000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr13:51467200-51468000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr13:51467200-51468200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr13:51467200-51468200	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr13:51467200-51468200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr13:51467200-51468400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr13:51467200-51468800	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr13:51467200-51468800	Enhancers	Brain Germinal Matrix	brain
43	chr13:51467200-51469000	Enhancers	Fetal Lung	lung
44	chr13:51467200-51469000	Enhancers	Fetal Muscle Leg	muscle
45	chr13:51467200-51469400	Enhancers	H9 Cell Line	embryonic stem cell
46	chr13:51467200-51470200	Flanking Active TSS	Dnd41	blood
47	chr13:51467400-51467600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr13:51467400-51467600	Flanking Active TSS	Primary B cells from peripheral blood	blood
49	chr13:51467400-51467600	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr13:51467400-51467800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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