Variant report

Variant	rs4555271
Chromosome Location	chr19:36610190-36610191
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	POLR2A	chr19:36610078-36612354	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36601583..36604210-chr19:36609754..36611847,2	MCF-7	breast:

Variant related genes	Relation type
TBCB	TF binding region
POLR2I	TF binding region
ENSG00000105261	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1009381	1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap]
rs10406862	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10418079	0.85[YRI][hapmap];0.87[ASN][1000 genomes]
rs10419924	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10422055	0.82[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs10425700	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10427033	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11538454	0.86[ASN][1000 genomes]
rs11666192	0.93[ASN][1000 genomes]
rs11669890	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12462159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12608517	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12981698	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[YRI][hapmap];0.85[ASN][1000 genomes]
rs2074435	1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.83[ASN][1000 genomes]
rs2075472	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2141959	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2227260	1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs2231568	0.92[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs2301734	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2301737	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2871649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4806249	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4806254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4806271	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4806273	0.83[ASN][1000 genomes]
rs4806276	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55849299	0.84[ASN][1000 genomes]
rs6510516	0.82[LWK][hapmap];0.89[YRI][hapmap]
rs7250364	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7251912	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7258807	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73036134	0.92[ASN][1000 genomes]
rs8112640	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]

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	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2752541	chr19:36563057-36690874	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4555271	CYP2A7	cis	parietal	SCAN
rs4555271	PHLDB3	cis	parietal	SCAN
rs4555271	ZNF527	cis	cerebellum	SCAN
rs4555271	POLR2I	cis	multi-tissue	Pritchard
rs4555271	ZFP36	cis	parietal	SCAN
rs4555271	ZNF420	cis	cerebellum	SCAN
rs4555271	PHLDB3	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36607200-36612200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:36607200-36612200	Weak transcription	Aorta	Aorta
3	chr19:36607200-36618600	Weak transcription	Psoas Muscle	Psoas
4	chr19:36607400-36612800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:36607400-36612800	Weak transcription	HSMMtube	muscle
6	chr19:36607400-36613800	Weak transcription	HSMM	muscle
7	chr19:36607400-36617000	Strong transcription	Thymus	Thymus
8	chr19:36607400-36617200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr19:36607400-36618400	Weak transcription	Stomach Mucosa	stomach
10	chr19:36607400-36618600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr19:36607400-36618800	Weak transcription	Small Intestine	intestine
12	chr19:36607600-36610400	Strong transcription	Fetal Intestine Large	intestine
13	chr19:36607600-36610600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr19:36607600-36610600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:36607600-36610800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr19:36607600-36611000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr19:36607600-36611000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr19:36607600-36611200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr19:36607600-36612000	Genic enhancers	Brain Inferior Temporal Lobe	brain
20	chr19:36607600-36612400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr19:36607600-36612400	Strong transcription	NHEK	skin
22	chr19:36607600-36614800	Weak transcription	HUVEC	blood vessel
23	chr19:36607600-36615400	Strong transcription	Fetal Lung	lung
24	chr19:36607600-36616000	Weak transcription	Fetal Kidney	kidney
25	chr19:36607600-36617000	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr19:36607600-36617000	Strong transcription	Primary T cells from cord blood	blood
27	chr19:36607600-36617000	Strong transcription	Brain Germinal Matrix	brain
28	chr19:36607600-36617000	Strong transcription	Fetal Muscle Leg	muscle
29	chr19:36607600-36617000	Strong transcription	Osteobl	bone
30	chr19:36607600-36617200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:36607600-36617200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr19:36607600-36617200	Strong transcription	Placenta	Placenta
33	chr19:36607600-36618400	Weak transcription	K562	blood
34	chr19:36607800-36610200	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr19:36607800-36610800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:36607800-36617000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:36608000-36610200	Weak transcription	Colonic Mucosa	Colon
38	chr19:36608000-36610200	Genic enhancers	HepG2	liver
39	chr19:36608000-36610400	Strong transcription	Dnd41	blood
40	chr19:36608000-36610800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:36608000-36611600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr19:36608000-36613200	Strong transcription	Fetal Thymus	thymus
43	chr19:36608000-36616800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:36608000-36617000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr19:36608000-36617000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr19:36608000-36617000	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr19:36608000-36617200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr19:36608000-36617200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr19:36608000-36617200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr19:36608000-36617200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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