Variant report

Variant	rs57879296
Chromosome Location	chr6:142893396-142893397
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11155253	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11155254	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12190036	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191805	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12191946	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12194448	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197895	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199515	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12202680	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203291	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203643	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203842	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12206762	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12208034	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208386	0.93[ASN][1000 genomes]
rs12208860	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12209687	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209912	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17071853	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17071855	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28883110	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4339484	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5005418	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55669522	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55786645	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57341971	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57589155	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57818992	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57876681	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58539996	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58697749	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59695424	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61126241	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6570519	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6929064	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73588317	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73588318	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73588321	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73590133	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73590163	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73590192	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73590199	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7746631	0.82[EUR][1000 genomes]
rs7751673	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755667	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756064	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7766583	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770363	0.85[EUR][1000 genomes];0.91[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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1023426	chr6:142813845-142940262	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830827	chr6:142840734-143015005	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv520479	chr6:142869099-142908146	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142888400-142893400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr6:142889200-142893600	Enhancers	Dnd41	blood
3	chr6:142889800-142893400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:142891200-142893400	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr6:142891400-142893800	Enhancers	Primary T cells from cord blood	blood
6	chr6:142891600-142895200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:142892200-142893400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:142892200-142895200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr6:142892800-142894000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:142893000-142893400	Enhancers	Stomach Mucosa	stomach
11	chr6:142893200-142893800	Enhancers	Fetal Intestine Small	intestine
12	chr6:142893200-142895000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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