Variant report

Variant	rs12405882
Chromosome Location	chr1:223576134-223576135
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223575712..223579320-chr1:223583036..223585021,3	MCF-7	breast:
2	chr1:223574260..223577674-chr1:223613937..223618124,4	MCF-7	breast:
3	chr1:223536303..223538270-chr1:223574488..223576964,2	K562	blood:
4	chr1:223575927..223578563-chr1:223880828..223883618,2	K562	blood:

Variant related genes	Relation type
ENSG00000143502	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10907375	0.88[ASN][1000 genomes]
rs11261265	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11261268	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11261269	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579995	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12064476	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12074609	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12074782	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12078619	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12082133	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12087387	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12094897	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1400964	0.88[ASN][1000 genomes]
rs1619161	0.82[EUR][1000 genomes]
rs1621030	0.80[ASN][1000 genomes]
rs1713213	0.82[EUR][1000 genomes]
rs17162005	0.88[ASN][1000 genomes]
rs17163836	0.88[ASN][1000 genomes]
rs1772288	0.82[EUR][1000 genomes]
rs1772289	0.82[EUR][1000 genomes]
rs1819706	0.82[EUR][1000 genomes]
rs1914612	0.87[ASN][1000 genomes]
rs2298063	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2353204	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2501982	0.89[EUR][1000 genomes]
rs2678369	0.82[EUR][1000 genomes]
rs28788929	0.88[ASN][1000 genomes]
rs28897212	0.88[ASN][1000 genomes]
rs34482638	0.88[AMR][1000 genomes]
rs35059272	0.88[AMR][1000 genomes]
rs35345617	0.88[ASN][1000 genomes]
rs35727959	0.88[ASN][1000 genomes]
rs35736338	0.88[ASN][1000 genomes]
rs35996176	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs59584296	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838211	0.88[AMR][1000 genomes]
rs61838233	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61838244	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61838245	0.81[ASN][1000 genomes]
rs6661314	0.88[ASN][1000 genomes]
rs6677044	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6679661	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6682552	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6689850	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6700523	0.88[ASN][1000 genomes]
rs6701453	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs825136	0.82[EUR][1000 genomes]
rs825137	0.82[EUR][1000 genomes]
rs825142	0.82[EUR][1000 genomes]
rs825143	0.82[EUR][1000 genomes]
rs825145	0.82[EUR][1000 genomes]
rs825146	0.82[EUR][1000 genomes]
rs825148	0.82[EUR][1000 genomes]
rs866637	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832670	chr1:223561771-223683381	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv4687	chr1:223565080-223610362	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223575000-223576600	Weak transcription	Primary T cells from cord blood	blood
2	chr1:223575000-223576800	Enhancers	Osteobl	bone
3	chr1:223575200-223576800	Enhancers	A549	lung
4	chr1:223575200-223577000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:223575200-223577000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:223575200-223577000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:223575200-223577000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:223575200-223577000	Enhancers	NH-A	brain
9	chr1:223575200-223577000	Enhancers	NHLF	lung
10	chr1:223575400-223576200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:223575400-223576600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:223575400-223576600	Enhancers	Muscle Satellite Cultured Cells	--
13	chr1:223575400-223576800	Enhancers	HSMM	muscle
14	chr1:223575400-223577000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:223575400-223577000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:223575400-223577000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:223575400-223577000	Enhancers	HMEC	breast
18	chr1:223575400-223577000	Enhancers	NHDF-Ad	bronchial
19	chr1:223575400-223577000	Enhancers	NHEK	skin
20	chr1:223575400-223577600	Enhancers	Hela-S3	cervix
21	chr1:223575600-223576200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:223575600-223576600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr1:223575600-223576800	Enhancers	HSMMtube	muscle
24	chr1:223575600-223578400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:223575800-223576600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:223575800-223577800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:223576000-223576600	Flanking Active TSS	K562	blood

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