Variant report

Variant	rs12060669
Chromosome Location	chr1:77790520-77790521
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11162313	0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12062661	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12085340	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12089711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12092582	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7529652	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9324160	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77777000-77794600	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr1:77779400-77794400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:77779600-77794600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:77785200-77794400	Weak transcription	Primary T cells from cord blood	blood
5	chr1:77785200-77799200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:77787200-77790600	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr1:77787600-77790600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:77787800-77790600	Enhancers	Brain Hippocampus Middle	brain
9	chr1:77788600-77798600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:77788600-77805800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:77788800-77813000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:77789000-77813000	Weak transcription	NHLF	lung
13	chr1:77789000-77831200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:77789600-77798600	Weak transcription	A549	lung
15	chr1:77789800-77800600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:77790000-77798600	Weak transcription	NHDF-Ad	bronchial
17	chr1:77790000-77808600	Weak transcription	HSMM	muscle
18	chr1:77790400-77790600	Enhancers	Brain Substantia Nigra	brain
19	chr1:77790400-77795200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:77790400-77804200	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links