Variant report

Variant	rs900688
Chromosome Location	chr3:47449058-47449059
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:6)
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	chr3:47448291-47450485	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:47448198-47450386	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr3:47449005-47449413	A549	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:47421193..47424069-chr3:47445764..47449832,6	MCF-7	breast:
2	chr3:47420808..47423598-chr3:47443683..47449500,5	K562	blood:
3	chr3:47432633..47435080-chr3:47446859..47450404,3	K562	blood:
4	chr3:47446881..47449586-chr3:47515417..47517364,2	K562	blood:
5	chr3:47431748..47433338-chr3:47447535..47449419,2	MCF-7	breast:
6	chr3:47425391..47427606-chr3:47448113..47450358,2	K562	blood:

No data

Variant related genes	Relation type
PTPN23	TF binding region
ENSG00000076201	Chromatin interaction
ENSG00000114650	Chromatin interaction
ENSG00000260236	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1024036	1.00[EUR][1000 genomes]
rs1038393	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10865945	1.00[EUR][1000 genomes]
rs10865947	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1091068	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11130134	0.89[AMR][1000 genomes]
rs11707272	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11922925	1.00[EUR][1000 genomes]
rs12488371	1.00[EUR][1000 genomes]
rs12631697	1.00[EUR][1000 genomes]
rs13077134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13078181	1.00[EUR][1000 genomes]
rs13323092	1.00[EUR][1000 genomes]
rs1531874	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1872165	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1874264	1.00[EUR][1000 genomes]
rs1979736	1.00[EUR][1000 genomes]
rs2170814	0.87[AMR][1000 genomes]
rs2350642	1.00[EUR][1000 genomes]
rs295431	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295432	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295434	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295443	1.00[EUR][1000 genomes]
rs295444	1.00[EUR][1000 genomes]
rs295445	1.00[EUR][1000 genomes]
rs295448	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295450	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295451	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295453	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295454	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295455	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295456	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295457	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295459	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs448018	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858812	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858823	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858834	0.89[AMR][1000 genomes]
rs4858855	0.87[AMR][1000 genomes]
rs4858896	1.00[EUR][1000 genomes]
rs6442062	1.00[EUR][1000 genomes]
rs6442063	1.00[EUR][1000 genomes]
rs6442066	1.00[EUR][1000 genomes]
rs6442068	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442069	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs648226	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6767868	1.00[EUR][1000 genomes]
rs6772449	1.00[EUR][1000 genomes]
rs6778673	1.00[EUR][1000 genomes]
rs6778687	1.00[EUR][1000 genomes]
rs6783591	1.00[EUR][1000 genomes]
rs6785538	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787210	1.00[EUR][1000 genomes]
rs6788978	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6789730	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808117	1.00[EUR][1000 genomes]
rs6808629	1.00[EUR][1000 genomes]
rs7372780	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831482	1.00[EUR][1000 genomes]
rs7615774	1.00[EUR][1000 genomes]
rs7621853	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7630154	1.00[EUR][1000 genomes]
rs7639121	1.00[EUR][1000 genomes]
rs7643150	1.00[EUR][1000 genomes]
rs7644043	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649413	1.00[EUR][1000 genomes]
rs7652492	1.00[EUR][1000 genomes]
rs807930	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs807933	1.00[EUR][1000 genomes]
rs900689	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900690	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900691	1.00[EUR][1000 genomes]
rs900692	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900694	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs924009	1.00[EUR][1000 genomes]
rs9826488	1.00[EUR][1000 genomes]
rs9828124	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828473	1.00[EUR][1000 genomes]
rs9852167	1.00[EUR][1000 genomes]
rs9861247	1.00[EUR][1000 genomes]
rs9861265	1.00[EUR][1000 genomes]
rs9869489	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	esv1807553	chr3:47393616-47470763	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47423800-47449800	Weak transcription	A549	lung
2	chr3:47426200-47462400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:47430200-47449600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:47436000-47454600	Weak transcription	Hela-S3	cervix
5	chr3:47436200-47462000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr3:47436600-47454800	Weak transcription	Fetal Kidney	kidney
7	chr3:47437000-47450000	Weak transcription	HUVEC	blood vessel
8	chr3:47437600-47453400	Weak transcription	Psoas Muscle	Psoas
9	chr3:47437800-47462800	Weak transcription	Fetal Brain Male	brain
10	chr3:47439200-47449200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:47439200-47455000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:47441000-47476800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:47441400-47462400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:47442000-47452800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr3:47444800-47459400	Strong transcription	Liver	Liver
16	chr3:47445000-47449800	Strong transcription	Primary B cells from cord blood	blood
17	chr3:47445000-47451400	Strong transcription	Primary T cells from cord blood	blood
18	chr3:47445000-47462000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr3:47445000-47462400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:47445000-47462800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:47445600-47462800	Strong transcription	Fetal Brain Female	brain
22	chr3:47445800-47455600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr3:47446000-47449600	Strong transcription	Thymus	Thymus
24	chr3:47446000-47450200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:47446000-47458400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:47446000-47462200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:47446000-47462800	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:47446200-47462000	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr3:47446200-47462800	Strong transcription	Dnd41	blood
30	chr3:47446400-47450600	Genic enhancers	Placenta	Placenta
31	chr3:47446400-47462800	Strong transcription	Colonic Mucosa	Colon
32	chr3:47446600-47449400	Genic enhancers	Esophagus	oesophagus
33	chr3:47446600-47456200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:47446600-47457400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:47446600-47462800	Strong transcription	Brain Germinal Matrix	brain
36	chr3:47446800-47449400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:47446800-47449600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:47446800-47459400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:47446800-47462000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:47446800-47462200	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr3:47447000-47450800	Strong transcription	Spleen	Spleen
42	chr3:47447000-47451200	Strong transcription	HepG2	liver
43	chr3:47447000-47451600	Strong transcription	GM12878-XiMat	blood
44	chr3:47447000-47452600	Weak transcription	NHDF-Ad	bronchial
45	chr3:47447000-47453200	Weak transcription	NH-A	brain
46	chr3:47447000-47454400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:47447000-47462400	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:47447000-47462400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:47447000-47462400	Weak transcription	Fetal Heart	heart
50	chr3:47447000-47462400	Strong transcription	NHLF	lung

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