Variant report

Variant	rs3809744
Chromosome Location	chr17:46507918-46507919
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	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	RUNX3	chr17:46507198-46507972	GM12878	blood:	n/a	n/a
5	POLR2A	chr17:46506507-46507983	GM12892	blood:	n/a	n/a
6	USF2	chr17:46507661-46508029	GM12878	blood:	n/a	n/a
7	POLR2A	chr17:46506736-46507948	GM19193	blood:	n/a	n/a
8	MTA3	chr17:46507593-46508032	GM12878	blood:	n/a	n/a
9	RUNX3	chr17:46507124-46508046	GM12878	blood:	n/a	n/a
10	MAX	chr17:46507162-46508061	HCT-116	colon:	n/a	chr17:46507697-46507704 chr17:46507696-46507705
11	POLR2A	chr17:46507335-46507949	MCF-7	breast:	n/a	n/a
12	YY1	chr17:46507140-46508058	GM12878	blood:	n/a	chr17:46507658-46507669
13	E2F6	chr17:46507226-46507959	H1-hESC	embryonic stem cell:	n/a	chr17:46507487-46507499 chr17:46507488-46507503 chr17:46507880-46507889
14	CTCF	chr17:46507800-46507950	GM12865	blood:	n/a	n/a
15	MAX	chr17:46507106-46507933	H1-hESC	embryonic stem cell:	n/a	chr17:46507697-46507704 chr17:46507696-46507705
16	MAX	chr17:46507191-46508011	ECC-1	luminal epithelium:	n/a	chr17:46507697-46507704 chr17:46507696-46507705
17	POLR2A	chr17:46507145-46507943	GM12878	blood:	n/a	n/a
18	RCOR1	chr17:46507158-46508091	GM12878	blood:	n/a	n/a
19	BHLHE40	chr17:46507388-46508007	GM12878	blood:	n/a	chr17:46507651-46507667
20	E2F6	chr17:46507089-46508018	H1-hESC	embryonic stem cell:	n/a	chr17:46507487-46507499 chr17:46507488-46507503 chr17:46507880-46507889
21	MAX	chr17:46507254-46508047	GM12878	blood:	n/a	chr17:46507697-46507704 chr17:46507696-46507705
22	ELF1	chr17:46507246-46508002	GM12878	blood:	n/a	n/a
23	MAX	chr17:46507479-46507949	MCF-7	breast:	n/a	chr17:46507697-46507704 chr17:46507696-46507705
24	POLR2A	chr17:46506537-46507933	GM12878	blood:	n/a	n/a
25	MXI1	chr17:46507119-46508060	GM12878	blood:	n/a	n/a
26	WRNIP1	chr17:46507863-46507947	GM12878	blood:	n/a	n/a
27	PAX5	chr17:46507242-46507996	GM12878	blood:	n/a	n/a
28	PML	chr17:46506658-46508323	GM12878	blood:	n/a	n/a
29	ELF1	chr17:46507239-46507993	GM12878	blood:	n/a	n/a
30	POLR2A	chr17:46507317-46507925	MCF-7	breast:	n/a	n/a
31	MAX	chr17:46507275-46507936	H1-hESC	embryonic stem cell:	n/a	chr17:46507697-46507704 chr17:46507696-46507705

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:46507895-46507945	SK-N-MC	brain:	n/a
2	chr17:46507895-46507945	U87	brain:	n/a
3	chr17:46507895-46507945	HepG2	liver:	n/a
4	chr17:46507895-46507945	ovcar-3	ovarian:	n/a
5	chr17:46507895-46507945	HEEpiC	esophagus:	n/a
6	chr17:46507895-46507945	AG10803	skin:	n/a
7	chr17:46507895-46507945	Caco-2	colon:	n/a
8	chr17:46507895-46507945	ECC-1	luminal epithelium:	n/a
9	chr17:46507895-46507945	Hepatocyte	liver:	n/a
10	chr17:46507895-46507945	MCF10A-Er-Src	breast:	n/a
11	chr17:46507895-46507945	AG04449	skin:	fetal
12	chr17:46507895-46507945	HCT-116	colon:	n/a
13	chr17:46507895-46507945	BE2_C	brain:	n/a
14	chr17:46507895-46507945	HIPEpiC	eye:	n/a
15	chr17:46507895-46507945	MCF-7	breast:	n/a
16	chr17:46507895-46507945	SK-N-SH	brain:	n/a
17	chr17:46507895-46507945	GM12878	blood:	n/a
18	chr17:46507895-46507945	HNPCEpiC	eye:	n/a
19	chr17:46507895-46507945	GM19239	blood:	n/a
20	chr17:46507895-46507945	GM12892	blood:	n/a
21	chr17:46507895-46507945	Hela-S3	cervix:	n/a
22	chr17:46507895-46507945	NT2-D1	testis:	n/a
23	chr17:46507895-46507945	GM06990	blood:	n/a
24	chr17:46507895-46507945	AG09309	skin:	n/a
25	chr17:46507895-46507945	K562	blood:	n/a
26	chr17:46507895-46507945	RPTEC	kidney:	n/a
27	chr17:46507895-46507945	SK-N-SH_RA	brain:	n/a
28	chr17:46507895-46507945	T-47D	breast:	n/a
29	chr17:46507895-46507945	AoSMC	blood vessel:	n/a
30	chr17:46507895-46507945	HEK293	kidney:	embryo
31	chr17:46507895-46507945	A549	lung:	n/a
32	chr17:46507895-46507945	HCM	heart:	n/a
33	chr17:46507895-46507945	HRCEpiC	kidney:	n/a
34	chr17:46507895-46507945	HAEpiC	amniotic membrane:	n/a
35	chr17:46507895-46507945	NHDF-neo	bronchial:	n/a
36	chr17:46507895-46507945	SKMC	muscle:	n/a
37	chr17:46507895-46507945	HCPEpiC	choroid plexus:	n/a
38	chr17:46507895-46507945	IMR90	lung:	fetal
39	chr17:46507895-46507945	HCF	heart:	n/a
40	chr17:46507895-46507945	PrEC	prostate:	n/a
41	chr17:46507895-46507945	SAEC	small airway:	n/a
42	chr17:46507895-46507945	PANC-1	pancreas:	n/a
43	chr17:46507895-46507945	NHBE	bronchial:	n/a
44	chr17:46507895-46507945	HRE	kidney:	n/a
45	chr17:46507895-46507945	HUVEC	blood vessel:	n/a
46	chr17:46507895-46507945	CMK	blood:	n/a
47	chr17:46507895-46507945	NH-A	brain:	n/a
48	chr17:46507895-46507945	AG04450	lung:	fetal
49	chr17:46507895-46507945	HMEC	breast:	n/a
50	chr17:46507895-46507945	H1-hESC	embryonic stem cell:	embryo

Variant related genes	Relation type
SKAP1	TF binding region
SKAP1	CpG island

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10514944	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1396869	0.93[ASN][1000 genomes]
rs16954324	0.87[AFR][1000 genomes]
rs16955960	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs16956001	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs16956501	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16957085	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16957299	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs17621689	0.89[AFR][1000 genomes]
rs17623125	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17623416	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17623518	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17694092	0.89[AFR][1000 genomes]
rs17694168	0.89[AFR][1000 genomes]
rs17694670	0.89[AFR][1000 genomes]
rs17695179	0.82[AMR][1000 genomes]
rs2036521	0.89[AFR][1000 genomes]
rs2175156	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2271264	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34463696	0.87[ASN][1000 genomes]
rs55641965	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55751709	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55765969	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55912545	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56011283	0.83[ASN][1000 genomes]
rs56093336	0.82[AMR][1000 genomes]
rs56103412	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56151068	0.82[AMR][1000 genomes]
rs56311919	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56371910	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72825596	0.89[AFR][1000 genomes]
rs72827810	0.89[AFR][1000 genomes]
rs72827825	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs72827848	0.82[AMR][1000 genomes]
rs72827851	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs72827854	0.89[AFR][1000 genomes]
rs72827869	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72827873	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72827897	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9899997	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9907565	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9913716	0.87[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:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46505000-46508000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr17:46505600-46508200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr17:46506000-46510200	Weak transcription	K562	blood
4	chr17:46506400-46508000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
5	chr17:46506400-46508000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
6	chr17:46506400-46508000	Flanking Active TSS	Fetal Thymus	thymus
7	chr17:46506600-46508000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr17:46506600-46508200	Enhancers	Gastric	stomach
9	chr17:46506800-46508000	Bivalent Enhancer	Fetal Brain Male	brain
10	chr17:46506800-46508200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
11	chr17:46507000-46508000	Bivalent Enhancer	Fetal Intestine Large	intestine
12	chr17:46507000-46508000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
13	chr17:46507000-46508200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr17:46507200-46508000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
15	chr17:46507200-46508000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr17:46507200-46508000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
17	chr17:46507200-46508000	Flanking Active TSS	Pancreas	Pancrea
18	chr17:46507200-46508200	Bivalent Enhancer	Stomach Mucosa	stomach
19	chr17:46507400-46508000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
20	chr17:46507400-46508000	Enhancers	Primary B cells from cord blood	blood
21	chr17:46507400-46508000	Bivalent/Poised TSS	NHEK	skin
22	chr17:46507400-46508200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
23	chr17:46507400-46508200	Bivalent Enhancer	Placenta	Placenta
24	chr17:46507600-46508000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr17:46507600-46508000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
26	chr17:46507600-46508000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr17:46507600-46508000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr17:46507600-46508000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr17:46507600-46508000	Flanking Active TSS	Colonic Mucosa	Colon
30	chr17:46507600-46508000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
31	chr17:46507600-46508000	Flanking Active TSS	Thymus	Thymus
32	chr17:46507600-46508200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
33	chr17:46507600-46508200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr17:46507600-46508200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr17:46507800-46508000	Flanking Bivalent TSS/Enh	ES-WA7 Cell Line	embryonic stem cell
36	chr17:46507800-46508000	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
37	chr17:46507800-46508000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
38	chr17:46507800-46508000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
39	chr17:46507800-46508000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
40	chr17:46507800-46508000	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr17:46507800-46508000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr17:46507800-46508000	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
43	chr17:46507800-46508000	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr17:46507800-46508000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr17:46507800-46508000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr17:46507800-46508000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr17:46507800-46508000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr17:46507800-46508000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr17:46507800-46508000	Bivalent Enhancer	Liver	Liver
50	chr17:46507800-46508000	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon

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