Variant report

Variant	rs12569104
Chromosome Location	chr1:77911854-77911855
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11800652	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[AFR][1000 genomes]
rs11810135	1.00[CEU][hapmap];0.84[AFR][1000 genomes]
rs12045755	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12046197	0.82[EUR][1000 genomes]
rs12048207	0.82[EUR][1000 genomes]
rs12564592	1.00[CEU][hapmap]
rs12564604	1.00[CEU][hapmap]
rs12566093	0.87[AFR][1000 genomes]
rs12568374	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs12568376	1.00[CEU][hapmap];0.84[AFR][1000 genomes]
rs17100791	1.00[CEU][hapmap]
rs17100850	1.00[CEU][hapmap]
rs2245189	1.00[CEU][hapmap]
rs2270539	1.00[CEU][hapmap]
rs2291689	1.00[CEU][hapmap]
rs2291690	1.00[CEU][hapmap]
rs28776274	0.82[EUR][1000 genomes]
rs28878211	0.82[EUR][1000 genomes]
rs55848622	0.84[AFR][1000 genomes]
rs56910202	0.84[AFR][1000 genomes]
rs57744162	0.81[AFR][1000 genomes]
rs57754896	0.84[AFR][1000 genomes]
rs57940344	0.84[AFR][1000 genomes]
rs59029032	0.84[AFR][1000 genomes]
rs59043705	0.84[AFR][1000 genomes]
rs59913458	0.81[AFR][1000 genomes]
rs60645967	0.84[AFR][1000 genomes]
rs61553470	0.84[AFR][1000 genomes]
rs74092623	0.84[AFR][1000 genomes]
rs74092624	0.84[AFR][1000 genomes]
rs74092627	0.84[AFR][1000 genomes]
rs74092641	0.84[AFR][1000 genomes]
rs74092642	0.84[AFR][1000 genomes]
rs74092644	0.84[AFR][1000 genomes]
rs74092645	0.84[AFR][1000 genomes]
rs74092649	0.84[AFR][1000 genomes]
rs74092650	0.84[AFR][1000 genomes]
rs74092651	0.84[AFR][1000 genomes]
rs74092654	0.84[AFR][1000 genomes]
rs74092655	0.84[AFR][1000 genomes]
rs7524107	0.84[AFR][1000 genomes]
rs7532905	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005183	chr1:77728990-77949309	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv535010	chr1:77728990-77949309	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1003714	chr1:77756861-77949309	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv1848735	chr1:77885282-77918347	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv871605	chr1:77889505-77918347	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv521371	chr1:77899640-77912969	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv462095	chr1:77903611-77951460	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv546592	chr1:77903611-77951460	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77872200-77913800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:77894200-77912400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:77894200-77912600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:77900200-77913600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:77904800-77912600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:77905200-77912400	Weak transcription	NHDF-Ad	bronchial
7	chr1:77907000-77916200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:77907400-77914000	Weak transcription	Brain Substantia Nigra	brain
9	chr1:77907800-77914000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:77907800-77927000	Weak transcription	HSMMtube	muscle
11	chr1:77908400-77915600	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:77908400-77916200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:77908800-77912400	Weak transcription	Primary T cells from cord blood	blood
14	chr1:77909200-77912600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr1:77911000-77925600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:77911200-77934000	Weak transcription	HSMM	muscle

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