Variant report

Variant	rs17017925
Chromosome Location	chr1:211849946-211849947
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr1:211849857-211850057	K562	blood:	n/a	n/a
2	CBX3	chr1:211848433-211849994	K562	blood:	n/a	n/a
3	E2F4	chr1:211849904-211850363	MCF10A-Er-Src	breast:	n/a	n/a
4	ZNF384	chr1:211848755-211850041	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:211849941-211849991	AG04450	lung:	fetal
2	chr1:211849941-211849991	AoSMC	blood vessel:	n/a
3	chr1:211849941-211849991	GM19239	blood:	n/a
4	chr1:211849941-211849991	GM06990	blood:	n/a
5	chr1:211849941-211849991	BE2_C	brain:	n/a
6	chr1:211849941-211849991	Caco-2	colon:	n/a
7	chr1:211849941-211849991	NB4	blood:	n/a
8	chr1:211849941-211849991	HPAEpiC	pulmonary alveolar:	n/a
9	chr1:211849941-211849991	NHBE	bronchial:	n/a
10	chr1:211849941-211849991	HRPEpiC	eye:	n/a
11	chr1:211849941-211849991	HAEpiC	amniotic membrane:	n/a
12	chr1:211849941-211849991	HUVEC	blood vessel:	n/a
13	chr1:211849941-211849991	GM12892	blood:	n/a
14	chr1:211849941-211849991	MCF10A-Er-Src	breast:	n/a
15	chr1:211849941-211849991	ProgFib	skin:	n/a
16	chr1:211849941-211849991	U87	brain:	n/a
17	chr1:211849941-211849991	HRCEpiC	kidney:	n/a
18	chr1:211849941-211849991	RPTEC	kidney:	n/a
19	chr1:211849941-211849991	HNPCEpiC	eye:	n/a
20	chr1:211849941-211849991	ECC-1	luminal epithelium:	n/a
21	chr1:211849941-211849991	GM12878	blood:	n/a
22	chr1:211849941-211849991	GM12891	blood:	n/a
23	chr1:211849941-211849991	AG09309	skin:	n/a
24	chr1:211849941-211849991	HMEC	breast:	n/a
25	chr1:211849941-211849991	AG09319	gingival:	n/a
26	chr1:211849941-211849991	IMR90	lung:	fetal
27	chr1:211849941-211849991	K562	blood:	n/a
28	chr1:211849941-211849991	SK-N-MC	brain:	n/a
29	chr1:211849941-211849991	SK-N-SH	brain:	n/a
30	chr1:211849941-211849991	AG04449	skin:	fetal
31	chr1:211849941-211849991	HRE	kidney:	n/a
32	chr1:211849941-211849991	HL-60	blood:	n/a
33	chr1:211849941-211849991	ovcar-3	ovarian:	n/a
34	chr1:211849941-211849991	HCT-116	colon:	n/a
35	chr1:211849941-211849991	CMK	blood:	n/a
36	chr1:211849941-211849991	SKMC	muscle:	n/a
37	chr1:211849941-211849991	PrEC	prostate:	n/a
38	chr1:211849941-211849991	HEK293	kidney:	embryo
39	chr1:211849941-211849991	HEEpiC	esophagus:	n/a
40	chr1:211849941-211849991	H1-hESC	embryonic stem cell:	embryo
41	chr1:211849941-211849991	HCF	heart:	n/a
42	chr1:211849941-211849991	Jurkat	blood:	n/a
43	chr1:211849941-211849991	A549	lung:	n/a
44	chr1:211849941-211849991	Hela-S3	cervix:	n/a
45	chr1:211849941-211849991	PANC-1	pancreas:	n/a
46	chr1:211849941-211849991	Hepatocyte	liver:	n/a
47	chr1:211849941-211849991	NH-A	brain:	n/a
48	chr1:211849941-211849991	SK-N-SH_RA	brain:	n/a
49	chr1:211849941-211849991	AG10803	skin:	n/a
50	chr1:211849941-211849991	HepG2	liver:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:211848085..211850808-chr1:212208417..212210048,2	K562	blood:
2	chr1:211751583..211753296-chr1:211847712..211850652,2	MCF-7	breast:
3	chr1:211848085..211850740-chr1:212207683..212210151,5	K562	blood:

No data

Variant related genes	Relation type
NEK2	TF binding region
NEK2	CpG island
ENSG00000143493	Chromatin interaction
ENSG00000143476	Chromatin interaction
ENSG00000170385	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs17017862	1.00[AMR][1000 genomes]
rs17017912	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17017917	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57174828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59680042	1.00[AMR][1000 genomes]
rs61557483	1.00[AMR][1000 genomes]
rs6661346	1.00[AMR][1000 genomes]
rs73075314	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73075316	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73075319	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73075326	1.00[AMR][1000 genomes]
rs73075338	1.00[AMR][1000 genomes]
rs73075364	1.00[AMR][1000 genomes]
rs73075368	1.00[AMR][1000 genomes]
rs73075374	1.00[AMR][1000 genomes]
rs73075379	1.00[AMR][1000 genomes]
rs73075380	1.00[AMR][1000 genomes]
rs73078726	1.00[AMR][1000 genomes]
rs73078738	1.00[AMR][1000 genomes]
rs73078742	1.00[AMR][1000 genomes]
rs73078769	1.00[AMR][1000 genomes]
rs7539737	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754845	chr1:211846605-211878605	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211847600-211850000	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr1:211847600-211850000	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr1:211847600-211850000	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr1:211848200-211850000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr1:211848200-211850000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr1:211848200-211850000	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr1:211848400-211850000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:211848400-211850000	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr1:211848600-211850000	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr1:211849400-211854000	Weak transcription	Primary T cells from cord blood	blood
11	chr1:211849400-211854000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:211849400-211854000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:211849400-211854000	Weak transcription	Brain Angular Gyrus	brain
14	chr1:211849400-211854400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:211849400-211854400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:211849600-211850000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:211849600-211850000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:211849600-211850000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:211849600-211850000	Enhancers	Placenta Amnion	Placenta Amnion
20	chr1:211849600-211850200	Flanking Active TSS	HepG2	liver
21	chr1:211849600-211850600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr1:211849600-211852200	Enhancers	Primary B cells from cord blood	blood
23	chr1:211849600-211852200	Enhancers	GM12878-XiMat	blood
24	chr1:211849600-211853400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:211849600-211853800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr1:211849600-211854000	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr1:211849600-211854000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:211849600-211854000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:211849600-211854000	Weak transcription	Brain Anterior Caudate	brain
30	chr1:211849600-211854000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:211849600-211854000	Weak transcription	Brain Hippocampus Middle	brain
32	chr1:211849600-211854000	Weak transcription	NH-A	brain
33	chr1:211849600-211854400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr1:211849600-211854400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:211849600-211854400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:211849600-211854400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:211849600-211854400	Weak transcription	Fetal Lung	lung
38	chr1:211849600-211854400	Weak transcription	HMEC	breast
39	chr1:211849800-211850000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
40	chr1:211849800-211850000	Flanking Active TSS	H9 Cell Line	embryonic stem cell
41	chr1:211849800-211850000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:211849800-211850000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr1:211849800-211850000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:211849800-211850000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:211849800-211850000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:211849800-211850000	Enhancers	Fetal Intestine Large	intestine
47	chr1:211849800-211850000	Enhancers	Hela-S3	cervix
48	chr1:211849800-211850200	Weak transcription	Brain Substantia Nigra	brain
49	chr1:211849800-211850200	Enhancers	Duodenum Mucosa	Duodenum
50	chr1:211849800-211850200	Enhancers	A549	lung

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