Variant report

Variant	rs16970988
Chromosome Location	chr17:33775820-33775821
allele	A/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	E2F6	chr17:33775248-33776313	H1-hESC	embryonic stem cell:	n/a	chr17:33775477-33775486 chr17:33775606-33775615
2	CREB1	chr17:33775077-33776224	GM12878	blood:	n/a	n/a
3	EP300	chr17:33775145-33776103	GM12878	blood:	n/a	chr17:33775590-33775606 chr17:33775589-33775605
4	POLR2A	chr17:33775083-33776257	GM12878	blood:	n/a	n/a
5	POLR2A	chr17:33775085-33776260	GM12892	blood:	n/a	n/a
6	MXI1	chr17:33775142-33776195	GM12878	blood:	n/a	n/a
7	NFYA	chr17:33775722-33776022	GM12878	blood:	n/a	n/a
8	SP1	chr17:33775658-33776030	GM12878	blood:	n/a	n/a
9	TBP	chr17:33775190-33776016	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr17:33775205-33776105	GM10847	blood:	n/a	n/a
11	YY1	chr17:33775612-33776029	GM12878	blood:	n/a	n/a
12	POLR2A	chr17:33775121-33776180	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr17:33775617-33776116	A549	lung:	n/a	n/a
14	BCLAF1	chr17:33775059-33776231	GM12878	blood:	n/a	chr17:33775602-33775615 chr17:33775607-33775616 chr17:33775584-33775597
15	POLR2A	chr17:33775119-33776935	GM19099	blood:	n/a	n/a
16	WRNIP1	chr17:33775706-33776256	GM12878	blood:	n/a	n/a
17	USF2	chr17:33775693-33776130	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr17:33775630-33775866	A549	lung:	n/a	n/a
19	POLR2A	chr17:33775053-33776379	GM12892	blood:	n/a	n/a
20	SIN3AK20	chr17:33775699-33775968	PANC-1	pancreas:	n/a	n/a
21	PAX5	chr17:33775066-33775943	GM12878	blood:	n/a	n/a
22	RUNX3	chr17:33774958-33776080	GM12878	blood:	n/a	chr17:33775345-33775362
23	E2F6	chr17:33775169-33776268	A549	lung:	n/a	chr17:33775477-33775486 chr17:33775606-33775615
24	MTA3	chr17:33775030-33776889	GM12878	blood:	n/a	n/a
25	POLR2A	chr17:33775139-33776835	GM15510	blood:	n/a	n/a
26	TBL1XR1	chr17:33775126-33775945	GM12878	blood:	n/a	n/a
27	TAF7	chr17:33775233-33775859	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr17:33775601-33775903	A549	lung:	n/a	n/a
29	ELF1	chr17:33774850-33776173	GM12878	blood:	n/a	n/a
30	SIN3AK20	chr17:33775157-33776189	PANC-1	pancreas:	n/a	n/a
31	E2F6	chr17:33775074-33777003	H1-hESC	embryonic stem cell:	n/a	chr17:33775477-33775486 chr17:33775606-33775615
32	STAT5A	chr17:33775070-33776141	GM12878	blood:	n/a	n/a
33	MAX	chr17:33775217-33776307	A549	lung:	n/a	n/a
34	POLR2A	chr17:33775134-33776940	GM18526	blood:	n/a	n/a
35	POLR2A	chr17:33775096-33776338	GM12878	blood:	n/a	n/a
36	POU2F2	chr17:33775091-33777021	GM12878	blood:	n/a	chr17:33775474-33775486 chr17:33775599-33775611 chr17:33775602-33775614 chr17:33776338-33776350 chr17:33775578-33775590 chr17:33775477-33775489 chr17:33776344-33776356
37	SP1	chr17:33775285-33776176	A549	lung:	n/a	chr17:33775475-33775487 chr17:33775606-33775615 chr17:33775607-33775616 chr17:33775602-33775616 chr17:33775477-33775486 chr17:33775605-33775617 chr17:33775476-33775485 chr17:33775605-33775617 chr17:33775476-33775490 chr17:33775606-33775616
38	GTF2F1	chr17:33775628-33776020	H1-hESC	embryonic stem cell:	n/a	n/a
39	TCF12	chr17:33775392-33776187	A549	lung:	n/a	n/a
40	POLR2A	chr17:33775086-33776229	GM12878	blood:	n/a	n/a
41	POLR2A	chr17:33775164-33776025	H1-hESC	embryonic stem cell:	n/a	n/a
42	MAX	chr17:33775233-33776235	H1-hESC	embryonic stem cell:	n/a	n/a
43	BHLHE40	chr17:33775151-33776052	GM12878	blood:	n/a	chr17:33775589-33775605
44	SP1	chr17:33775493-33776138	H1-hESC	embryonic stem cell:	n/a	chr17:33775606-33775615 chr17:33775607-33775616 chr17:33775602-33775616 chr17:33775605-33775617 chr17:33775605-33775617 chr17:33775606-33775616
45	POLR2A	chr17:33774687-33776084	GM12891	blood:	n/a	n/a
46	STAT1	chr17:33775805-33775985	GM12878	blood:	n/a	n/a
47	GABPA	chr17:33774985-33775854	HL-60	blood:	n/a	chr17:33775606-33775615
48	MAX	chr17:33775567-33776271	H1-hESC	embryonic stem cell:	n/a	n/a
49	BACH1	chr17:33775498-33775873	H1-hESC	embryonic stem cell:	n/a	n/a
50	REST	chr17:33775148-33776013	HL-60	blood:	n/a	chr17:33775792-33775805

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:33775779-33775829	AG09309	skin:	n/a
2	chr17:33775779-33775829	HMEC	breast:	n/a
3	chr17:33775779-33775829	IMR90	lung:	fetal
4	chr17:33775779-33775829	GM12878	blood:	n/a
5	chr17:33775779-33775829	HRCEpiC	kidney:	n/a
6	chr17:33775779-33775829	HNPCEpiC	eye:	n/a
7	chr17:33775779-33775829	HepG2	liver:	n/a
8	chr17:33775779-33775829	ECC-1	luminal epithelium:	n/a
9	chr17:33775779-33775829	HRPEpiC	eye:	n/a
10	chr17:33775779-33775829	BE2_C	brain:	n/a
11	chr17:33775779-33775829	Hepatocyte	liver:	n/a
12	chr17:33775779-33775829	HEK293	kidney:	embryo
13	chr17:33775779-33775829	ovcar-3	ovarian:	n/a
14	chr17:33775779-33775829	MCF-7	breast:	n/a
15	chr17:33775779-33775829	HL-60	blood:	n/a
16	chr17:33775779-33775829	NHBE	bronchial:	n/a
17	chr17:33775779-33775829	GM19239	blood:	n/a
18	chr17:33775779-33775829	HEEpiC	esophagus:	n/a
19	chr17:33775779-33775829	NT2-D1	testis:	n/a
20	chr17:33775779-33775829	SK-N-SH_RA	brain:	n/a
21	chr17:33775779-33775829	SKMC	muscle:	n/a
22	chr17:33775779-33775829	HUVEC	blood vessel:	n/a
23	chr17:33775779-33775829	HPAEpiC	pulmonary alveolar:	n/a
24	chr17:33775779-33775829	U87	brain:	n/a
25	chr17:33775779-33775829	PFSK-1	brain:	n/a
26	chr17:33775779-33775829	T-47D	breast:	n/a
27	chr17:33775779-33775829	GM06990	blood:	n/a
28	chr17:33775779-33775829	AoSMC	blood vessel:	n/a
29	chr17:33775779-33775829	HIPEpiC	eye:	n/a
30	chr17:33775779-33775829	H1-hESC	embryonic stem cell:	embryo
31	chr17:33775779-33775829	Hela-S3	cervix:	n/a
32	chr17:33775779-33775829	PANC-1	pancreas:	n/a
33	chr17:33775779-33775829	GM12892	blood:	n/a
34	chr17:33775779-33775829	A549	lung:	n/a
35	chr17:33775779-33775829	CMK	blood:	n/a
36	chr17:33775779-33775829	PrEC	prostate:	n/a
37	chr17:33775779-33775829	LNCaP	prostate:	n/a
38	chr17:33775779-33775829	HCPEpiC	choroid plexus:	n/a
39	chr17:33775779-33775829	HCM	heart:	n/a
40	chr17:33775779-33775829	Jurkat	blood:	n/a
41	chr17:33775779-33775829	HCT-116	colon:	n/a
42	chr17:33775779-33775829	BJ	skin:	n/a
43	chr17:33775779-33775829	SK-N-SH	brain:	n/a
44	chr17:33775779-33775829	Caco-2	colon:	n/a
45	chr17:33775779-33775829	GM12891	blood:	n/a
46	chr17:33775779-33775829	NB4	blood:	n/a
47	chr17:33775779-33775829	AG04450	lung:	fetal
48	chr17:33775779-33775829	HCF	heart:	n/a
49	chr17:33775779-33775829	RPTEC	kidney:	n/a
50	chr17:33775779-33775829	MCF10A-Er-Src	breast:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:33769997..33772468-chr17:33774210..33776177,2	K562	blood:
2	chr17:33775239..33775823-chr2:28974546..28975384,2	NB4	blood:

Variant related genes	Relation type
SLFN13	TF binding region
SLFN13	CpG island
ENSG00000154760	Chromatin interaction
ENSG00000213639	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12450604	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12451141	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12451679	0.91[EUR][1000 genomes]
rs12453650	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12601267	1.00[AFR][1000 genomes]
rs16971025	1.00[ASW][hapmap];1.00[MEX][hapmap];0.86[EUR][1000 genomes]
rs16971028	1.00[ASW][hapmap];1.00[AFR][1000 genomes]
rs3785758	1.00[AFR][1000 genomes]
rs62078109	0.83[EUR][1000 genomes]
rs62078141	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62078142	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62078145	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62078151	0.91[EUR][1000 genomes]
rs62078154	0.91[EUR][1000 genomes]
rs7225005	0.81[EUR][1000 genomes]
rs72483216	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8065626	0.81[JPT][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055936	chr17:33327166-33884184	Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
2	nsv543317	chr17:33327166-33884184	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
3	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv574741	chr17:33552275-33827134	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
5	nsv1056116	chr17:33691457-33815452	Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	esv3432530	chr17:33738621-33802241	Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33774200-33777200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr17:33774400-33777000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr17:33774600-33776000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr17:33774600-33776000	Active TSS	H9 Cell Line	embryonic stem cell
5	chr17:33774600-33776000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
6	chr17:33774600-33776000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr17:33774600-33776000	Active TSS	HMEC	breast
8	chr17:33774600-33776800	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr17:33774800-33776000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr17:33774800-33776000	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr17:33774800-33776000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr17:33774800-33776000	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr17:33774800-33776000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
14	chr17:33774800-33776400	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr17:33774800-33776400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr17:33774800-33776400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr17:33774800-33776600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr17:33774800-33776600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr17:33774800-33776600	Active TSS	Duodenum Mucosa	Duodenum
20	chr17:33774800-33776800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
21	chr17:33774800-33776800	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr17:33774800-33776800	Active TSS	Colon Smooth Muscle	Colon
23	chr17:33774800-33776800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
24	chr17:33775000-33776200	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
25	chr17:33775000-33776400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr17:33775000-33776400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
27	chr17:33775000-33776800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
28	chr17:33775000-33777000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr17:33775000-33777000	Active TSS	Aorta	Aorta
30	chr17:33775200-33776000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr17:33775200-33776000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr17:33775200-33776000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr17:33775200-33776000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
34	chr17:33775200-33776000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
35	chr17:33775200-33776000	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
36	chr17:33775200-33776000	Bivalent/Poised TSS	Stomach Mucosa	stomach
37	chr17:33775200-33776000	Bivalent/Poised TSS	NHEK	skin
38	chr17:33775200-33776200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr17:33775200-33776200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr17:33775200-33776200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
41	chr17:33775200-33776600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr17:33775200-33776800	Active TSS	Gastric	stomach
43	chr17:33775200-33776800	Bivalent/Poised TSS	NHDF-Ad	bronchial
44	chr17:33775200-33776800	Bivalent/Poised TSS	NHLF	lung
45	chr17:33775200-33777000	Bivalent Enhancer	Fetal Brain Male	brain
46	chr17:33775400-33776000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
47	chr17:33775400-33776000	Flanking Bivalent TSS/Enh	Left Ventricle	heart
48	chr17:33775400-33776000	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
49	chr17:33775400-33776000	Flanking Bivalent TSS/Enh	Osteobl	bone
50	chr17:33775400-33776200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links