Variant report

Variant	rs4806276
Chromosome Location	chr19:36599967-36599968
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:36599871-36600191	MCF-7	breast:	n/a	n/a
2	POLR2A	chr19:36599747-36600003	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr19:36596983-36603152	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:36599814-36600287	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr19:36596929-36600393	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr19:36599418-36600061	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr19:36597069-36600450	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr19:36593610-36600036	PANC-1	pancreas:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:36597873..36601557-chr19:36602123..36605335,7	K562	blood:
2	chr19:36596596..36601731-chr19:36602791..36606754,6	K562	blood:
3	chr19:36588129..36590741-chr19:36597182..36600281,3	MCF-7	breast:
4	chr19:36593756..36597019-chr19:36598726..36601991,4	K562	blood:
5	chr19:36487223..36488748-chr19:36599253..36601474,2	K562	blood:
6	chr19:36594277..36596518-chr19:36598748..36601596,3	MCF-7	breast:

No data

Variant related genes	Relation type
OVOL3	TF binding region
ENSG00000105261	Chromatin interaction
ENSG00000105258	Chromatin interaction
ENSG00000105254	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1009381	1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
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];1.00[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10418079	0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs10419924	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10420345	0.85[ASN][1000 genomes]
rs10422055	0.82[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.87[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];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];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10427033	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11538454	0.93[ASN][1000 genomes]
rs11666192	1.00[ASN][1000 genomes]
rs11669890	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[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];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12981698	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[YRI][hapmap]
rs2023866	0.84[ASN][1000 genomes]
rs2074435	1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2075472	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2141959	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2227260	1.00[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2231568	0.92[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2285745	0.82[EUR][1000 genomes]
rs2301734	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2301737	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2871649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4555271	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]
rs4806249	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4806254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4806262	0.85[ASN][1000 genomes]
rs4806271	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4806273	0.89[ASN][1000 genomes]
rs55849299	0.91[ASN][1000 genomes]
rs6510516	0.82[LWK][hapmap];0.89[YRI][hapmap]
rs7250364	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7251912	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][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];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73036134	0.99[ASN][1000 genomes]
rs8112640	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4806276	CYP2A7	cis	parietal	SCAN
rs4806276	PHLDB3	cis	cerebellum	SCAN
rs4806276	PHLDB3	cis	parietal	SCAN
rs4806276	ZNF527	cis	cerebellum	SCAN
rs4806276	ZNF420	cis	cerebellum	SCAN
rs4806276	ZFP36	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36546600-36602200	Weak transcription	Colonic Mucosa	Colon
2	chr19:36546600-36604800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr19:36546800-36601400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr19:36556000-36601600	Weak transcription	Pancreas	Pancrea
5	chr19:36568800-36601400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr19:36571800-36600000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr19:36571800-36600600	Strong transcription	Fetal Stomach	stomach
8	chr19:36572400-36602400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr19:36573800-36602400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:36574200-36602000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr19:36574600-36604400	Weak transcription	NHDF-Ad	bronchial
12	chr19:36575400-36604200	Weak transcription	Primary B cells from cord blood	blood
13	chr19:36585000-36601600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr19:36585000-36602400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr19:36585200-36604400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr19:36588400-36604800	Weak transcription	NH-A	brain
17	chr19:36590200-36600200	Strong transcription	Fetal Brain Female	brain
18	chr19:36590200-36604600	Strong transcription	Fetal Intestine Small	intestine
19	chr19:36590400-36605000	Weak transcription	Aorta	Aorta
20	chr19:36590600-36604800	Weak transcription	Psoas Muscle	Psoas
21	chr19:36592200-36602400	Weak transcription	Brain Substantia Nigra	brain
22	chr19:36592400-36604800	Weak transcription	Right Atrium	heart
23	chr19:36593200-36602600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr19:36593400-36603400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:36594000-36602400	Weak transcription	Fetal Lung	lung
26	chr19:36594000-36603400	Weak transcription	Hela-S3	cervix
27	chr19:36594200-36602400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr19:36594400-36601400	Weak transcription	Liver	Liver
29	chr19:36594800-36603600	Weak transcription	Colon Smooth Muscle	Colon
30	chr19:36594800-36604400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr19:36595000-36601800	Weak transcription	Gastric	stomach
32	chr19:36595000-36602600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr19:36595000-36603600	Weak transcription	HepG2	liver
34	chr19:36595200-36600000	Strong transcription	Brain Cingulate Gyrus	brain
35	chr19:36595200-36601400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr19:36595600-36603400	Weak transcription	Brain Angular Gyrus	brain
37	chr19:36595600-36603400	Weak transcription	HSMM	muscle
38	chr19:36595600-36603400	Weak transcription	HUVEC	blood vessel
39	chr19:36595600-36604000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr19:36595800-36604000	Weak transcription	HMEC	breast
41	chr19:36596200-36601400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr19:36596200-36601600	Weak transcription	Adipose Nuclei	Adipose
43	chr19:36596200-36603400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr19:36596200-36603800	Weak transcription	GM12878-XiMat	blood
45	chr19:36596200-36604000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:36596400-36601000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr19:36596400-36601400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr19:36596400-36601400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr19:36596400-36601400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr19:36596400-36601600	Weak transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links