Variant report

Variant	rs12088041
Chromosome Location	chr1:56070444-56070445
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1039295	1.00[EUR][1000 genomes]
rs10493193	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10493194	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10493196	0.83[YRI][hapmap]
rs11206626	0.89[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs11206627	0.82[ASN][1000 genomes]
rs11206645	1.00[EUR][1000 genomes]
rs1165460	1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12059018	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12068867	1.00[EUR][1000 genomes]
rs12071564	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076746	1.00[EUR][1000 genomes]
rs12081733	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1392137	1.00[EUR][1000 genomes]
rs17112410	1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17112413	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17112456	0.85[YRI][hapmap]
rs28475680	1.00[EUR][1000 genomes]
rs59236443	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59539072	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60149406	1.00[EUR][1000 genomes]
rs6588567	1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs6670673	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs6677373	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680818	1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs7416182	1.00[EUR][1000 genomes]
rs7520444	1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7548272	1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv10184	chr1:55728755-56084833	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv461617	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv546303	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv1014866	chr1:56059054-56129092	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56059600-56076000	Weak transcription	Aorta	Aorta
2	chr1:56063200-56089000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:56067400-56071200	Weak transcription	Ovary	ovary
4	chr1:56069200-56070800	Enhancers	NHDF-Ad	bronchial
5	chr1:56069600-56071400	Enhancers	Fetal Heart	heart
6	chr1:56069600-56072000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:56069800-56070800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:56069800-56071000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:56070000-56070600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:56070000-56071600	Enhancers	Adipose Nuclei	Adipose
11	chr1:56070200-56076200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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