Variant report

Variant	rs11079804
Chromosome Location	chr17:46020698-46020699
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:46020462-46020707	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr17:46020199-46023291	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr17:46020640-46021851	HepG2	liver:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45970912..45974701-chr17:46018890..46021752,3	K562	blood:
2	chr17:46018061..46020719-chr17:46045036..46046879,2	K562	blood:
3	chr17:45968434..45977260-chr17:46017847..46029594,27	MCF-7	breast:
4	chr17:45915810..45917332-chr17:46018370..46020809,2	K562	blood:
5	chr17:46017765..46021634-chr17:46045854..46051133,6	MCF-7	breast:
6	chr17:45993643..45995953-chr17:46019014..46020704,3	MCF-7	breast:
7	chr17:45971510..45977679-chr17:46016123..46021422,20	MCF-7	breast:
8	chr17:46019148..46022019-chr17:46092699..46095180,2	K562	blood:
9	chr17:45978341..45980674-chr17:46019226..46022209,2	MCF-7	breast:
10	chr17:45945622..45948288-chr17:46019914..46021881,2	MCF-7	breast:
11	chr17:45973201..45977546-chr17:46016018..46021091,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000263798	TF binding region
PNPO	TF binding region
ENSG00000234494	TF binding region
ENSG00000108465	Chromatin interaction
ENSG00000141295	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000264920	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1108833	0.84[CHB][hapmap]
rs11545723	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11654010	0.83[CHB][hapmap]
rs12452082	0.94[MEX][hapmap]
rs12948368	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1476578	0.88[CHB][hapmap]
rs1476579	0.88[CHB][hapmap]
rs17617250	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074191	0.94[MEX][hapmap]
rs2525087	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs2525088	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs2525090	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs2525093	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs2525096	0.88[CHB][hapmap]
rs2525098	0.88[CHB][hapmap]
rs2597171	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs2597172	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs2597173	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs2597174	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs2597179	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs2875746	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs2905851	0.86[CHB][hapmap]
rs2905852	0.88[CHB][hapmap]
rs3096	0.80[MKK][hapmap]
rs34428844	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35004787	0.83[AMR][1000 genomes]
rs35132293	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35480192	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35533494	0.83[AMR][1000 genomes]
rs4793693	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4793734	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4794225	0.82[CEU][hapmap];0.94[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56119022	0.83[AMR][1000 genomes]
rs62067368	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs66721410	0.83[AMR][1000 genomes]
rs7211859	0.84[CHB][hapmap]
rs7220419	0.94[MEX][hapmap]
rs729785	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs729786	0.88[CHB][hapmap]
rs737130	0.88[CHB][hapmap]
rs739853	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs7503584	0.88[CHB][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap]
rs757061	0.94[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1062503	chr17:45977445-46021384	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11079804	PNPO	cis	parietal	SCAN
rs11079804	ASB16	cis	parietal	SCAN
rs11079804	HOXB2	cis	multi-tissue	Pritchard
rs11079804	NFE2L1	cis	parietal	SCAN
rs11079804	ETV4	cis	parietal	SCAN
rs11079804	PNPO	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46019600-46027000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:46019800-46020800	Enhancers	Pancreas	Pancrea
3	chr17:46019800-46020800	Flanking Active TSS	HepG2	liver
4	chr17:46019800-46021200	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr17:46019800-46021200	Weak transcription	Lung	lung
6	chr17:46019800-46021600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr17:46019800-46021800	Enhancers	Primary T cells fromperipheralblood	blood
8	chr17:46019800-46021800	Enhancers	Thymus	Thymus
9	chr17:46019800-46022200	Weak transcription	Right Ventricle	heart
10	chr17:46019800-46022600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr17:46019800-46022600	Weak transcription	Right Atrium	heart
12	chr17:46019800-46022800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr17:46019800-46022800	Weak transcription	Gastric	stomach
14	chr17:46019800-46022800	Weak transcription	Psoas Muscle	Psoas
15	chr17:46019800-46023400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr17:46019800-46024000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr17:46019800-46024800	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr17:46019800-46025600	Weak transcription	HSMM	muscle
19	chr17:46019800-46026800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr17:46019800-46026800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr17:46019800-46026800	Weak transcription	Brain Germinal Matrix	brain
22	chr17:46019800-46026800	Weak transcription	HSMMtube	muscle
23	chr17:46019800-46027400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr17:46019800-46034200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr17:46019800-46047600	Weak transcription	Aorta	Aorta
26	chr17:46020000-46020800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr17:46020000-46020800	Enhancers	Adipose Nuclei	Adipose
28	chr17:46020000-46020800	Enhancers	Brain Anterior Caudate	brain
29	chr17:46020000-46020800	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr17:46020000-46020800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr17:46020000-46021000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr17:46020000-46021000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr17:46020000-46021000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr17:46020000-46021000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr17:46020000-46021200	Enhancers	Fetal Intestine Large	intestine
36	chr17:46020000-46021600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr17:46020000-46021600	Weak transcription	Fetal Stomach	stomach
38	chr17:46020000-46021800	Weak transcription	Fetal Muscle Leg	muscle
39	chr17:46020000-46021800	Weak transcription	Spleen	Spleen
40	chr17:46020000-46022000	Enhancers	Primary T cells from cord blood	blood
41	chr17:46020000-46022000	Weak transcription	Colonic Mucosa	Colon
42	chr17:46020000-46022200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr17:46020000-46022200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr17:46020000-46022200	Weak transcription	Brain Angular Gyrus	brain
45	chr17:46020000-46022200	Weak transcription	Brain Hippocampus Middle	brain
46	chr17:46020000-46022200	Weak transcription	Esophagus	oesophagus
47	chr17:46020000-46022200	Weak transcription	Fetal Brain Female	brain
48	chr17:46020000-46022200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr17:46020000-46022400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr17:46020000-46022600	Weak transcription	NHLF	lung

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