Variant report

Variant	rs479117
Chromosome Location	chr4:75025369-75025370
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBL1XR1	chr4:75025349-75025508	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:75022682-75025406	HUVEC	blood vessel:	n/a	n/a
3	BRCA1	chr4:75023014-75025411	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr4:75022256-75036597	K562	blood:	n/a	n/a
5	POLR2A	chr4:75022788-75025384	Hela-S3	cervix:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:74964506..74967065-chr4:75022087..75025561,3	K562	blood:
2	chr4:75023332..75025369-chr4:75145514..75147366,2	MCF-7	breast:
3	chr4:75022872..75025434-chr4:75174456..75176612,2	MCF-7	breast:
4	chr4:75025200..75026058-chr5:28474351..28475312,2	Hela-S3	cervix:
5	chr4:74920487..74923421-chr4:75023614..75026198,3	K562	blood:
6	chr4:75024505..75027399-chr4:75144223..75145811,2	K562	blood:
7	chr4:74528064..74529636-chr4:75024964..75026974,2	K562	blood:
8	chr4:75024456..75026319-chr4:75184021..75186282,2	K562	blood:
9	chr4:75024221..75026156-chr4:75163622..75165985,2	K562	blood:
10	chr4:74964506..74968474-chr4:75022087..75025768,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000269559	TF binding region
ENSG00000248848	Chromatin interaction
ENSG00000182585	Chromatin interaction
ENSG00000081041	Chromatin interaction
ENSG00000163738	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10518119	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10938110	0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11942036	1.00[EUR][1000 genomes]
rs11946885	1.00[EUR][1000 genomes]
rs11947475	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1261917	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1440405	1.00[EUR][1000 genomes]
rs1440406	1.00[EUR][1000 genomes]
rs16850579	1.00[EUR][1000 genomes]
rs16850585	1.00[EUR][1000 genomes]
rs16850798	1.00[TSI][hapmap]
rs16850845	1.00[TSI][hapmap]
rs16850933	1.00[TSI][hapmap]
rs4694665	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs474734	0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs507061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs522698	0.80[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs536780	0.82[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs552357	0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55946357	1.00[EUR][1000 genomes]
rs56000473	1.00[EUR][1000 genomes]
rs56006412	1.00[EUR][1000 genomes]
rs56236141	1.00[EUR][1000 genomes]
rs56896590	1.00[EUR][1000 genomes]
rs569187	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs569206	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60336088	1.00[EUR][1000 genomes]
rs60633195	1.00[EUR][1000 genomes]
rs6833925	1.00[EUR][1000 genomes]
rs6841682	0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6850735	1.00[EUR][1000 genomes]
rs73824406	1.00[EUR][1000 genomes]
rs73824413	1.00[EUR][1000 genomes]
rs73824415	1.00[EUR][1000 genomes]
rs73824419	1.00[EUR][1000 genomes]
rs73824429	1.00[EUR][1000 genomes]
rs73827550	1.00[EUR][1000 genomes]
rs73827558	1.00[EUR][1000 genomes]
rs73827561	1.00[EUR][1000 genomes]
rs73827562	1.00[EUR][1000 genomes]
rs7681620	1.00[EUR][1000 genomes]
rs7687073	1.00[EUR][1000 genomes]
rs922136	1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1004768	chr4:74774372-75109579	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1006218	chr4:74782324-75105424	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv594683	chr4:75013441-75106485	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1013260	chr4:75013441-75121643	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1002907	chr4:75013441-75131443	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1004706	chr4:75014770-75121643	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv594684	chr4:75015750-75106485	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	esv3346537	chr4:75022913-75025461	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:75022800-75025400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr4:75023000-75025800	Active TSS	A549	lung
3	chr4:75023200-75025400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:75023200-75025400	Active TSS	Psoas Muscle	Psoas
5	chr4:75023200-75025400	Active TSS	Right Ventricle	heart
6	chr4:75023400-75025400	Active TSS	H9 Cell Line	embryonic stem cell
7	chr4:75023400-75025400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr4:75023400-75025400	Active TSS	HSMMtube	muscle
9	chr4:75023400-75025800	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr4:75023400-75025800	Active TSS	Hela-S3	cervix
11	chr4:75023600-75025400	Active TSS	Brain Germinal Matrix	brain
12	chr4:75023800-75025400	Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr4:75024200-75025400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr4:75024200-75025400	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr4:75024200-75025400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:75024200-75025400	Active TSS	Right Atrium	heart
17	chr4:75024200-75025800	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr4:75024200-75025800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:75024400-75025400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr4:75024400-75025800	Enhancers	Spleen	Spleen
21	chr4:75024400-75032400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:75024600-75025400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:75024600-75025400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
24	chr4:75024600-75025600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr4:75024600-75025600	Flanking Active TSS	Dnd41	blood
26	chr4:75024600-75025800	Enhancers	Small Intestine	intestine
27	chr4:75024600-75025800	Flanking Active TSS	HUVEC	blood vessel
28	chr4:75024600-75030400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr4:75024600-75034000	Weak transcription	Gastric	stomach
30	chr4:75024800-75025400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr4:75024800-75025400	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr4:75024800-75025400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:75024800-75025400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr4:75024800-75025400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:75024800-75025400	Flanking Active TSS	GM12878-XiMat	blood
36	chr4:75024800-75025400	Flanking Active TSS	NHEK	skin
37	chr4:75024800-75025800	Enhancers	Primary B cells from cord blood	blood
38	chr4:75024800-75025800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr4:75024800-75026400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr4:75024800-75026400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:75024800-75027000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr4:75024800-75029000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr4:75024800-75032000	Weak transcription	Placenta	Placenta
44	chr4:75024800-75032400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr4:75024800-75032600	Weak transcription	Lung	lung
46	chr4:75024800-75033800	Weak transcription	Esophagus	oesophagus
47	chr4:75024800-75033800	Weak transcription	Stomach Mucosa	stomach
48	chr4:75024800-75034400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:75024800-75037000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr4:75024800-75056600	Weak transcription	Pancreas	Pancrea

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