Variant report

Variant	rs28413063
Chromosome Location	chr17:46508016-46508017
allele	C/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	MTA3	chr17:46506328-46508302	GM12878	blood:	n/a	n/a
2	MAX	chr17:46507184-46508047	ECC-1	luminal epithelium:	n/a	chr17:46507697-46507704 chr17:46507696-46507705
3	POLR2A	chr17:46506435-46508046	GM12878	blood:	n/a	n/a
4	USF2	chr17:46507661-46508029	GM12878	blood:	n/a	n/a
5	MTA3	chr17:46507593-46508032	GM12878	blood:	n/a	n/a
6	RUNX3	chr17:46507124-46508046	GM12878	blood:	n/a	n/a
7	MAX	chr17:46507162-46508061	HCT-116	colon:	n/a	chr17:46507697-46507704 chr17:46507696-46507705
8	YY1	chr17:46507140-46508058	GM12878	blood:	n/a	chr17:46507658-46507669
9	RCOR1	chr17:46507158-46508091	GM12878	blood:	n/a	n/a
10	E2F6	chr17:46507089-46508018	H1-hESC	embryonic stem cell:	n/a	chr17:46507487-46507499 chr17:46507488-46507503 chr17:46507880-46507889
11	MAX	chr17:46507254-46508047	GM12878	blood:	n/a	chr17:46507697-46507704 chr17:46507696-46507705
12	MXI1	chr17:46507119-46508060	GM12878	blood:	n/a	n/a
13	POLR2A	chr17:46508008-46508017	Gliobla	brain:	n/a	n/a
14	PML	chr17:46506658-46508323	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
SKAP1	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1027894	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11079819	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11079820	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1110921	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11650663	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654288	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655120	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655137	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11656589	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12449743	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12449855	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12451731	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12452277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12452566	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12452848	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12453784	1.00[ASN][1000 genomes]
rs16954446	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1973576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28436607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28577013	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28613168	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35772538	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4132677	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56727666	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57559912	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59042469	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6504259	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207949	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208499	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208758	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7212398	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213936	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7214922	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215843	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7217664	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219155	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7221156	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7222296	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7222830	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7224936	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7225940	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7226288	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8065457	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs8069796	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8070322	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8071222	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8073671	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8073979	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8079940	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8081430	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8082050	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9747388	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9891857	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9895449	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9897131	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9902082	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9904494	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9906587	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9909089	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9910351	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9911663	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9911712	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9914121	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9914154	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9915778	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9916572	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9916667	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833469	chr17:46491849-46709406	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
2	esv2761960	chr17:46504489-46529846	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	esv3420538	chr17:46504944-46861553	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	369 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46505600-46508200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr17:46506000-46510200	Weak transcription	K562	blood
3	chr17:46506600-46508200	Enhancers	Gastric	stomach
4	chr17:46506800-46508200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
5	chr17:46507000-46508200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr17:46507200-46508200	Bivalent Enhancer	Stomach Mucosa	stomach
7	chr17:46507400-46508200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr17:46507400-46508200	Bivalent Enhancer	Placenta	Placenta
9	chr17:46507600-46508200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
10	chr17:46507600-46508200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr17:46507600-46508200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
12	chr17:46507800-46508200	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
13	chr17:46507800-46508200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr17:46507800-46508200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
15	chr17:46507800-46508200	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr17:46507800-46508200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr17:46507800-46508200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr17:46507800-46508200	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
19	chr17:46507800-46508200	Flanking Active TSS	GM12878-XiMat	blood
20	chr17:46507800-46508400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr17:46508000-46508200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr17:46508000-46508200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr17:46508000-46508200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr17:46508000-46508200	Enhancers	Colonic Mucosa	Colon
25	chr17:46508000-46508200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
26	chr17:46508000-46508200	Enhancers	Pancreas	Pancrea
27	chr17:46508000-46508200	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
28	chr17:46508000-46508200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
29	chr17:46508000-46508200	Flanking Bivalent TSS/Enh	Spleen	Spleen
30	chr17:46508000-46508400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
31	chr17:46508000-46508400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
32	chr17:46508000-46508400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr17:46508000-46508400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
34	chr17:46508000-46508400	Bivalent Enhancer	Fetal Kidney	kidney
35	chr17:46508000-46508400	Enhancers	Thymus	Thymus
36	chr17:46508000-46508600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr17:46508000-46508600	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr17:46508000-46508800	Bivalent Enhancer	Primary B cells from cord blood	blood
39	chr17:46508000-46509200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr17:46508000-46509400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr17:46508000-46509600	Enhancers	Primary T cells fromperipheralblood	blood
42	chr17:46508000-46509800	Enhancers	Fetal Thymus	thymus
43	chr17:46508000-46511800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr17:46508000-46517000	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr17:46508000-46517800	Enhancers	Primary T helper cells fromperipheralblood	blood

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