Variant report

Variant	rs9880633
Chromosome Location	chr3:111453414-111453415
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:111452077..111454237-chr3:111460686..111462940,2	K562	blood:
2	chr3:111448052..111452466-chr3:111452775..111456031,4	MCF-7	breast:
3	chr3:111452923..111457246-chr3:111577346..111581538,6	MCF-7	breast:
4	chr3:111448469..111451104-chr3:111452736..111455582,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144824	Chromatin interaction
ENSG00000240891	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs12632310	0.82[CEU][hapmap]
rs13317985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13321524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs13322494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs13325336	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17423838	0.81[CEU][hapmap]
rs17489748	0.81[CEU][hapmap];0.80[YRI][hapmap]
rs2292516	0.82[CEU][hapmap]
rs28479130	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28534728	0.93[EUR][1000 genomes]
rs28648833	0.93[EUR][1000 genomes]
rs28675079	0.83[EUR][1000 genomes]
rs3821919	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3922706	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3922707	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3922780	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4075549	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4276156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4390898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs4516581	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4542994	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4634085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs4682313	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56052712	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56215064	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57902958	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58124137	0.93[EUR][1000 genomes]
rs58663746	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60867472	0.93[EUR][1000 genomes]
rs6438012	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs66651424	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66786213	0.93[EUR][1000 genomes]
rs66856712	0.93[EUR][1000 genomes]
rs66975684	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6762246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6762572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6778818	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs6782513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6787278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6789977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6790355	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6790521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6790612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6790825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6790977	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs6795947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67970120	0.83[EUR][1000 genomes]
rs6798476	0.82[JPT][hapmap]
rs6800047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6800065	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6800922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6802960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs73220212	0.87[ASN][1000 genomes]
rs73222475	0.93[EUR][1000 genomes]
rs73222500	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7614433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7627909	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9842396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9843288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs9850748	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9858064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9858228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9862472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9868898	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9871034	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9877777	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591290	chr3:111427455-111462570	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111415200-111454200	Weak transcription	Small Intestine	intestine
2	chr3:111427600-111456000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:111442000-111454200	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr3:111442400-111456000	Weak transcription	Lung	lung
5	chr3:111442800-111455800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:111443200-111454800	Weak transcription	Primary T cells from cord blood	blood
7	chr3:111444200-111456000	Weak transcription	Aorta	Aorta
8	chr3:111445200-111456800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:111448800-111453600	Weak transcription	Right Atrium	heart
10	chr3:111448800-111454200	Weak transcription	Adipose Nuclei	Adipose
11	chr3:111449000-111453600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:111449000-111453600	Weak transcription	HUVEC	blood vessel
13	chr3:111449000-111454200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:111449000-111455800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:111449200-111453600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:111449200-111453600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:111449400-111456000	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:111449600-111453600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:111449600-111453800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:111449600-111453800	Weak transcription	NHLF	lung
21	chr3:111449600-111456000	Weak transcription	Esophagus	oesophagus
22	chr3:111449800-111453600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:111449800-111453600	Weak transcription	NHDF-Ad	bronchial
24	chr3:111451200-111453600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:111451200-111454400	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr3:111451600-111453600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:111451600-111460400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:111452200-111454200	Flanking Active TSS	A549	lung
29	chr3:111452200-111458200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:111452400-111454000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr3:111452400-111454800	Enhancers	Fetal Intestine Large	intestine
32	chr3:111452400-111455000	Enhancers	Stomach Mucosa	stomach
33	chr3:111452400-111456000	Weak transcription	Gastric	stomach
34	chr3:111452400-111458800	Enhancers	HMEC	breast
35	chr3:111452600-111454600	Flanking Active TSS	HepG2	liver
36	chr3:111452600-111455800	Weak transcription	Fetal Stomach	stomach
37	chr3:111452600-111457200	Enhancers	HSMM	muscle
38	chr3:111452800-111453600	Enhancers	Hela-S3	cervix
39	chr3:111452800-111454000	Enhancers	Muscle Satellite Cultured Cells	--
40	chr3:111452800-111454800	Enhancers	Placenta	Placenta
41	chr3:111452800-111459200	Enhancers	Osteobl	bone
42	chr3:111452800-111460400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:111453000-111453800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:111453000-111454200	Enhancers	Pancreas	Pancrea
45	chr3:111453000-111459400	Enhancers	Placenta Amnion	Placenta Amnion
46	chr3:111453200-111453600	Enhancers	NHEK	skin
47	chr3:111453200-111456200	Weak transcription	Fetal Kidney	kidney
48	chr3:111453400-111453600	Enhancers	NH-A	brain
49	chr3:111453400-111453800	Flanking Active TSS	Liver	Liver
50	chr3:111453400-111454000	Enhancers	Fetal Heart	heart

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