Variant report

Variant	rs16949720
Chromosome Location	chr17:46027257-46027258
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	RCOR1	chr17:46026763-46027498	GM12878	blood:	n/a	n/a
2	NFIC	chr17:46027215-46027581	GM12878	blood:	n/a	n/a
3	MAX	chr17:46025809-46027314	A549	lung:	n/a	n/a
4	CTCF	chr17:46026037-46027397	HCT-116	colon:	n/a	chr17:46026781-46026802 chr17:46026782-46026795 chr17:46026780-46026796 chr17:46026779-46026797
5	POLR2A	chr17:46025886-46028079	HepG2	liver:	n/a	n/a
6	EP300	chr17:46026755-46027525	GM12878	blood:	n/a	n/a
7	STAT5A	chr17:46026517-46027627	GM12878	blood:	n/a	n/a
8	IKZF1	chr17:46026675-46027551	GM12878	blood:	n/a	n/a
9	POLR2A	chr17:46026691-46027314	PFSK-1	brain:	n/a	n/a
10	RUNX3	chr17:46026595-46027284	GM12878	blood:	n/a	n/a
11	CTCF	chr17:46026195-46027293	HCT-116	colon:	n/a	chr17:46026781-46026802 chr17:46026782-46026795 chr17:46026780-46026796 chr17:46026779-46026797
12	RAD21	chr17:46026024-46027275	HCT-116	colon:	n/a	chr17:46026780-46026799
13	ELF1	chr17:46025871-46027669	MCF-7	breast:	n/a	chr17:46027412-46027423
14	MAX	chr17:46025916-46027747	MCF-7	breast:	n/a	n/a
15	BCL3	chr17:46025893-46027407	A549	lung:	n/a	n/a
16	BCL3	chr17:46025853-46027404	A549	lung:	n/a	n/a
17	EBF1	chr17:46026634-46027742	GM12878	blood:	n/a	chr17:46027577-46027588
18	POLR2A	chr17:46025953-46027582	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr17:46025867-46027977	MCF-7	breast:	n/a	n/a
20	RELA	chr17:46026694-46027592	GM18951	blood:	n/a	n/a
21	RAD21	chr17:46026246-46027274	MCF-7	breast:	n/a	chr17:46026780-46026799
22	CHD1	chr17:46026572-46027300	GM12878	blood:	n/a	n/a
23	EP300	chr17:46026710-46027666	GM12878	blood:	n/a	n/a
24	RAD21	chr17:46026095-46027764	SK-N-SH	brain:	n/a	chr17:46026780-46026799
25	CTCF	chr17:46027120-46027270	GM12873	blood:	n/a	n/a
26	TCF12	chr17:46025757-46027305	A549	lung:	n/a	n/a
27	POLR2A	chr17:46027081-46027443	K562	blood:	n/a	n/a
28	SPI1	chr17:46027245-46027532	GM12878	blood:	n/a	chr17:46027412-46027421 chr17:46027411-46027424 chr17:46027410-46027423
29	RUNX3	chr17:46027224-46027615	GM12878	blood:	n/a	n/a
30	MTA3	chr17:46026386-46027751	GM12878	blood:	n/a	n/a
31	SMC3	chr17:46025869-46027855	SK-N-SH	brain:	n/a	chr17:46026781-46026795
32	CTCF	chr17:46025931-46027875	A549	lung:	n/a	chr17:46026781-46026802 chr17:46026782-46026795 chr17:46026780-46026796 chr17:46026779-46026797
33	MAZ	chr17:46026200-46027375	IMR90	lung:	n/a	n/a
34	NFIC	chr17:46025974-46027316	HepG2	liver:	n/a	n/a
35	POLR2A	chr17:46025923-46028067	HepG2	liver:	n/a	n/a
36	SPI1	chr17:46026646-46027440	GM12878	blood:	n/a	chr17:46027412-46027421 chr17:46027411-46027424 chr17:46027410-46027423
37	CTCF	chr17:46025857-46027841	SK-N-SH	brain:	n/a	chr17:46026781-46026802 chr17:46026782-46026795 chr17:46026780-46026796 chr17:46026779-46026797
38	FOSL2	chr17:46025826-46027645	A549	lung:	n/a	n/a
39	PML	chr17:46025834-46027617	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46026779..46027394-chr17:46048123..46048973,2	MCF-7	breast:
2	chr17:46026192..46029068-chr17:46087372..46089166,2	K562	blood:
3	chr17:45970281..45975378-chr17:46022719..46027732,11	MCF-7	breast:
4	chr17:46026023..46027620-chr17:46047369..46048630,14	MCF-7	breast:
5	chr17:46023026..46029175-chr17:46044937..46051234,10	K562	blood:
6	chr17:46026487..46027340-chr17:46047277..46048606,6	K562	blood:
7	chr17:45968434..45977260-chr17:46017847..46029594,27	MCF-7	breast:
8	chr17:46026764..46027682-chr17:46095633..46096284,2	MCF-7	breast:
9	chr17:46027110..46029262-chr17:46094448..46097370,2	MCF-7	breast:
10	chr17:45920063..45920877-chr17:46026748..46027498,2	K562	blood:
11	chr17:46026275..46027381-chr17:46055414..46056451,4	MCF-7	breast:
12	chr17:46026020..46027520-chr17:46047710..46048729,27	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264019	TF binding region
ENSG00000264920	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000108465	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11079802	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs11651753	0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs16949418	0.90[JPT][hapmap]
rs2002136	0.92[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2325748	0.90[JPT][hapmap]
rs2428608	0.85[ASN][1000 genomes]
rs2525095	0.82[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2525109	0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]
rs2525110	0.83[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs2597169	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2875735	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3764398	0.84[ASN][1000 genomes]
rs3826396	0.90[ASN][1000 genomes]
rs4793738	0.92[ASN][1000 genomes]
rs4794331	0.88[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs57768342	0.87[ASN][1000 genomes]
rs61665404	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7207225	0.95[JPT][hapmap]
rs7220104	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs72823505	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	esv1000014	chr17:46019228-46029457	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16949720	PNPO	cis	Nerve Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46019800-46027400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr17:46019800-46034200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:46019800-46047600	Weak transcription	Aorta	Aorta
4	chr17:46020000-46034600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr17:46023200-46030000	Genic enhancers	Fetal Intestine Large	intestine
6	chr17:46024400-46031600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr17:46025400-46027600	Genic enhancers	HMEC	breast
8	chr17:46025800-46027400	Genic enhancers	Fetal Stomach	stomach
9	chr17:46025800-46027400	Transcr. at gene 5' and 3'	HepG2	liver
10	chr17:46025800-46027600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr17:46026000-46027400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr17:46026000-46027600	Enhancers	Fetal Heart	heart
13	chr17:46026000-46027800	Enhancers	Primary B cells from cord blood	blood
14	chr17:46026000-46028000	Enhancers	Esophagus	oesophagus
15	chr17:46026200-46027600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr17:46026200-46027600	Enhancers	Left Ventricle	heart
17	chr17:46026200-46027600	Enhancers	Ovary	ovary
18	chr17:46026200-46027800	Enhancers	Primary B cells from peripheral blood	blood
19	chr17:46026200-46028000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
20	chr17:46026400-46027400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr17:46026400-46027400	Enhancers	Fetal Brain Male	brain
22	chr17:46026400-46027400	Flanking Active TSS	Rectal Smooth Muscle	rectum
23	chr17:46026400-46027600	Flanking Active TSS	Liver	Liver
24	chr17:46026400-46027600	Enhancers	Dnd41	blood
25	chr17:46026400-46027600	Flanking Active TSS	GM12878-XiMat	blood
26	chr17:46026400-46027600	Enhancers	HSMM	muscle
27	chr17:46026400-46028000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr17:46026400-46028000	Enhancers	Placenta	Placenta
29	chr17:46026600-46027400	Enhancers	Lung	lung
30	chr17:46026600-46027600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr17:46026600-46027600	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
32	chr17:46026600-46027800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr17:46026800-46027400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr17:46026800-46027400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr17:46026800-46027400	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr17:46026800-46027400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr17:46026800-46027400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr17:46026800-46027400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr17:46026800-46027400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr17:46026800-46027400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr17:46026800-46027400	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr17:46026800-46027400	Flanking Active TSS	Brain Angular Gyrus	brain
43	chr17:46026800-46027400	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr17:46026800-46027400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr17:46026800-46027400	Flanking Active TSS	Thymus	Thymus
46	chr17:46026800-46027400	Enhancers	HSMMtube	muscle
47	chr17:46026800-46027600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr17:46026800-46027600	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr17:46026800-46027600	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr17:46026800-46027600	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum

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