Variant report

Variant	rs9828260
Chromosome Location	chr3:110533465-110533466
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:110531400..110533494-chr3:110558447..110560628,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10511291	0.96[EUR][1000 genomes]
rs10755069	0.98[ASN][1000 genomes]
rs12493974	1.00[EUR][1000 genomes]
rs1350930	1.00[ASN][1000 genomes]
rs1350932	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1350979	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1381830	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1381833	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1381834	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1381835	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1381836	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1462299	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1462308	1.00[ASN][1000 genomes]
rs1462326	0.92[ASN][1000 genomes]
rs1462798	1.00[EUR][1000 genomes]
rs1462802	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1542513	1.00[ASN][1000 genomes]
rs1599576	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16857350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16857358	0.84[ASN][1000 genomes]
rs16857373	0.82[EUR][1000 genomes]
rs16857536	0.96[EUR][1000 genomes]
rs1870926	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2045784	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2169497	0.94[ASN][1000 genomes]
rs2169565	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2219706	1.00[EUR][1000 genomes]
rs2399364	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2399369	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4682024	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4682025	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4682027	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60037602	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6437934	1.00[EUR][1000 genomes]
rs6763050	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72934030	0.96[EUR][1000 genomes]
rs72934034	0.96[EUR][1000 genomes]
rs72934100	0.96[EUR][1000 genomes]
rs72935934	0.96[EUR][1000 genomes]
rs72948740	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72948795	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72948800	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7629008	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7650516	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs936512	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs969940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9839231	1.00[EUR][1000 genomes]
rs9881407	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9883216	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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	nsv1010230	chr3:110204439-110588814	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv536688	chr3:110204439-110588814	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1011034	chr3:110209344-110559021	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv536689	chr3:110209344-110559021	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv1014199	chr3:110293896-110754155	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3402004	chr3:110533262-110540960	Enhancers Flanking Active TSS Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110531400-110534400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:110532000-110533800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:110532000-110534400	Enhancers	HUVEC	blood vessel
4	chr3:110532000-110534800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:110532200-110534200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:110532200-110534400	Enhancers	HMEC	breast
7	chr3:110532400-110534200	Enhancers	NHEK	skin
8	chr3:110532400-110534400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:110532400-110535200	Enhancers	NHDF-Ad	bronchial
10	chr3:110532600-110533800	Enhancers	HSMMtube	muscle
11	chr3:110532600-110534200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:110532600-110534200	Enhancers	A549	lung
13	chr3:110532600-110534200	Enhancers	Hela-S3	cervix
14	chr3:110532800-110534200	Flanking Active TSS	NH-A	brain
15	chr3:110532800-110535000	Enhancers	Dnd41	blood
16	chr3:110533000-110533600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:110533000-110534200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:110533000-110534400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:110533000-110535200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:110533200-110533800	Enhancers	GM12878-XiMat	blood
21	chr3:110533200-110534200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:110533200-110534400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:110533200-110534400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr3:110533400-110533600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:110533400-110533800	Flanking Active TSS	NHLF	lung
26	chr3:110533400-110534000	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr3:110533400-110534000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr3:110533400-110534000	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr3:110533400-110534200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:110533400-110534200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:110533400-110534200	Flanking Active TSS	HSMM	muscle
32	chr3:110533400-110534200	Flanking Active TSS	Osteobl	bone
33	chr3:110533400-110534400	Enhancers	Stomach Mucosa	stomach
34	chr3:110533400-110534800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links