Variant report

Variant	rs302966
Chromosome Location	chr6:25069363-25069364
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:25056580..25058139-chr6:25068953..25070477,2	K562	blood:
2	chr6:25062051..25064646-chr6:25068488..25070452,3	K562	blood:
3	chr6:25067750..25069802-chr6:25071192..25073072,2	K562	blood:

Variant related genes	Relation type
ENSG00000230372	Chromatin interaction
ENSG00000223623	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1002596	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs159988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16890104	0.88[JPT][hapmap];0.87[YRI][hapmap]
rs2028973	0.88[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs2166682	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2166683	0.89[JPT][hapmap]
rs2394363	0.83[ASN][1000 genomes]
rs302973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs302983	0.88[JPT][hapmap]
rs302987	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs302991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs303000	0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs303004	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs303006	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs303007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs303008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs303009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs303016	0.88[JPT][hapmap]
rs303018	0.88[JPT][hapmap]
rs303026	0.88[JPT][hapmap]
rs3792970	0.88[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs3792971	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3792986	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3818268	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs391626	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs392852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs398672	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs420369	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4711077	0.85[ASN][1000 genomes]
rs4711078	0.81[ASN][1000 genomes]
rs57304238	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs57796643	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6906102	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs715426	0.80[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs715427	0.86[ASN][1000 genomes]
rs9295646	1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs9295647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9356961	0.86[ASN][1000 genomes]
rs9358833	0.86[ASN][1000 genomes]
rs9393617	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9654585	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs302966	CMAH	Cis_1M	lymphoblastoid	RTeQTL
rs302966	CMAHP	cis	Thyroid	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25057600-25080400	Weak transcription	Thymus	Thymus
2	chr6:25063000-25070800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:25063200-25070800	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:25063200-25079200	Weak transcription	Ovary	ovary
5	chr6:25065000-25069400	Weak transcription	NHDF-Ad	bronchial
6	chr6:25066400-25070800	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr6:25067400-25080400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:25067600-25070800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:25067600-25084600	Weak transcription	HSMMtube	muscle
10	chr6:25067800-25070600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:25068200-25069800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:25068400-25069800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:25069000-25069800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr6:25069000-25070400	Enhancers	Adipose Nuclei	Adipose
15	chr6:25069200-25069800	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links