Variant report

Variant	rs16880669
Chromosome Location	chr5:52327807-52327808
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:52319764..52321344-chr5:52327151..52329228,2	K562	blood:
2	chr5:52326404..52328383-chr5:52333260..52335027,2	MCF-7	breast:
3	chr5:52313064..52315275-chr5:52327348..52329688,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10940290	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1126643	0.91[YRI][hapmap]
rs11959632	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12521915	0.83[CEU][hapmap];0.87[YRI][hapmap]
rs12652168	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12657429	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12657501	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12657972	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12657980	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1316250	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1363192	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1421937	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1445943	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1862191	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2303122	0.83[CEU][hapmap]
rs3212424	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3212438	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3212439	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3212441	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3212450	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3212453	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3212455	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3212457	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3212458	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3212461	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3212464	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3212467	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3212472	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3212478	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3212480	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3212481	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3212486	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3756537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776787	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3797496	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3797498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3822558	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3926397	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62357232	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62357233	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67719154	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6880055	0.83[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7725246	0.87[YRI][hapmap]
rs989073	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv880425	chr5:52291279-52345868	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv881652	chr5:52323568-52385312	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52307000-52333800	Weak transcription	Gastric	stomach
2	chr5:52314200-52328600	Weak transcription	Lung	lung
3	chr5:52314200-52348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:52317600-52333600	Weak transcription	Colonic Mucosa	Colon
5	chr5:52318400-52331800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:52322200-52333200	Weak transcription	Fetal Stomach	stomach
7	chr5:52323200-52329000	Enhancers	NHLF	lung
8	chr5:52323600-52332600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr5:52324200-52334200	Weak transcription	Spleen	Spleen
10	chr5:52324400-52328800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:52324400-52356400	Weak transcription	Brain Anterior Caudate	brain
12	chr5:52324600-52332400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr5:52325400-52329200	Enhancers	HUVEC	blood vessel
14	chr5:52326000-52328400	Enhancers	Duodenum Mucosa	Duodenum
15	chr5:52326200-52328000	Enhancers	Colon Smooth Muscle	Colon
16	chr5:52326200-52328800	Enhancers	NH-A	brain
17	chr5:52326400-52328800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr5:52326400-52328800	Enhancers	HepG2	liver
19	chr5:52326400-52329200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:52326400-52329400	Enhancers	Dnd41	blood
21	chr5:52326400-52329400	Enhancers	Hela-S3	cervix
22	chr5:52326600-52328000	Enhancers	Stomach Mucosa	stomach
23	chr5:52326600-52328400	Enhancers	Brain Cingulate Gyrus	brain
24	chr5:52326600-52329200	Enhancers	NHDF-Ad	bronchial
25	chr5:52326800-52328200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:52326800-52328400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:52326800-52328400	Enhancers	Brain Substantia Nigra	brain
28	chr5:52326800-52328400	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr5:52326800-52328800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:52326800-52328800	Enhancers	Fetal Lung	lung
31	chr5:52326800-52329000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr5:52326800-52329400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr5:52327000-52328200	Flanking Active TSS	A549	lung
34	chr5:52327000-52328400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr5:52327000-52328600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:52327000-52328800	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr5:52327000-52328800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:52327000-52329000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:52327000-52329200	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr5:52327200-52328400	Enhancers	Brain Hippocampus Middle	brain
41	chr5:52327200-52328800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:52327200-52328800	Enhancers	Primary T cells from cord blood	blood
43	chr5:52327200-52329200	Enhancers	HMEC	breast
44	chr5:52327400-52328000	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr5:52327400-52328000	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr5:52327400-52328000	Enhancers	Fetal Intestine Small	intestine
47	chr5:52327400-52328000	Enhancers	Fetal Thymus	thymus
48	chr5:52327400-52328000	Enhancers	HSMM	muscle
49	chr5:52327400-52328800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr5:52327400-52328800	Enhancers	Primary T helper cells fromperipheralblood	blood

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