Variant report

Variant	rs12406000
Chromosome Location	chr1:98239710-98239711
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:98239660-98239810	MCF-7	breast:	n/a	n/a
2	CTCF	chr1:98239600-98239750	GM12874	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000230718	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10157611	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs1023245	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1034215	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs1034216	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1034217	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10493894	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10493895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10493896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10747485	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10747486	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs10747487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10783076	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10875105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs10875108	0.83[AMR][1000 genomes]
rs11165897	1.00[CHB][hapmap]
rs11165908	0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs11165913	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12073839	1.00[CHB][hapmap]
rs12406752	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12565244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12739159	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1333717	1.00[CHB][hapmap]
rs13375516	1.00[CHB][hapmap]
rs17369919	1.00[CHB][hapmap]
rs17378455	1.00[CHB][hapmap]
rs17378671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17379095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1889229	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1931063	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs1931064	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1931066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1974203	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs1974204	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1984091	0.80[EUR][1000 genomes]
rs2151563	1.00[CHB][hapmap]
rs2297595	1.00[CHB][hapmap]
rs2786490	1.00[CHB][hapmap]
rs2786498	1.00[CHB][hapmap]
rs2786500	1.00[CHB][hapmap]
rs2786501	1.00[CHB][hapmap]
rs2786503	1.00[CHB][hapmap]
rs2786505	1.00[CHB][hapmap]
rs2786509	1.00[CHB][hapmap]
rs2811194	1.00[CHB][hapmap]
rs2811195	1.00[CHB][hapmap]
rs2811196	1.00[CHB][hapmap]
rs2811198	1.00[CHB][hapmap]
rs2811199	1.00[CHB][hapmap]
rs2811200	1.00[CHB][hapmap]
rs2811202	1.00[CHB][hapmap]
rs2811203	1.00[CHB][hapmap]
rs34486749	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3790387	1.00[CHB][hapmap]
rs3790389	1.00[CHB][hapmap]
rs4304627	1.00[CHB][hapmap]
rs4329543	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4537601	0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs4970728	1.00[CHB][hapmap]
rs61786604	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61786605	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6663670	1.00[CHB][hapmap]
rs6668296	1.00[CHB][hapmap]
rs6675325	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6676451	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6683957	1.00[CHB][hapmap]
rs6685266	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6703307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7512910	1.00[CHB][hapmap]
rs7527085	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533039	chr1:97665736-98343102	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv530049	chr1:97883261-98384614	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1012958	chr1:98081528-98864746	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv871740	chr1:98165091-98322379	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv871472	chr1:98165091-98342417	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv870596	chr1:98165091-98365310	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv871625	chr1:98165091-98564736	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv871050	chr1:98187755-98365310	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	esv1799805	chr1:98198206-98349028	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv871651	chr1:98200719-98365310	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:98177200-98254600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:98183600-98279600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:98187200-98243400	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr1:98204000-98256600	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:98204200-98257000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:98207000-98254800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr1:98224800-98241000	Weak transcription	Gastric	stomach
8	chr1:98228400-98255200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:98229800-98240800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:98231200-98241600	Weak transcription	HSMM	muscle
11	chr1:98231200-98257800	Weak transcription	Small Intestine	intestine
12	chr1:98231400-98240800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr1:98231400-98245200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:98231600-98241800	Weak transcription	Liver	Liver
15	chr1:98236200-98241400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:98236400-98252000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:98237800-98241800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr1:98238000-98243600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr1:98238400-98240800	Weak transcription	Thymus	Thymus
20	chr1:98238600-98256600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:98239000-98239800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:98239000-98239800	ZNF genes & repeats	Lung	lung
23	chr1:98239000-98240000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:98239000-98240200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:98239000-98240200	ZNF genes & repeats	Fetal Lung	lung
26	chr1:98239000-98240400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
27	chr1:98239000-98240400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:98239000-98240600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
29	chr1:98239200-98239800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:98239200-98239800	ZNF genes & repeats	Primary B cells from cord blood	blood
31	chr1:98239200-98239800	ZNF genes & repeats	Adipose Nuclei	Adipose
32	chr1:98239200-98239800	ZNF genes & repeats	Brain Angular Gyrus	brain
33	chr1:98239200-98240000	Strong transcription	Primary T cells from cord blood	blood
34	chr1:98239400-98240800	Strong transcription	Dnd41	blood
35	chr1:98239600-98239800	ZNF genes & repeats	Pancreas	Pancrea
36	chr1:98239600-98240000	ZNF genes & repeats	Fetal Muscle Leg	muscle
37	chr1:98239600-98240200	ZNF genes & repeats	NHDF-Ad	bronchial

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