Variant report

Variant	rs12029642
Chromosome Location	chr1:79983877-79983878
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10874038	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12021904	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12023367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12023913	1.00[TSI][hapmap]
rs12025658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12026767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12027888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12027892	0.96[ASN][1000 genomes]
rs12028685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12030013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12030299	1.00[AMR][1000 genomes]
rs12034665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12036690	1.00[AFR][1000 genomes]
rs12036905	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12037641	1.00[AMR][1000 genomes]
rs12039488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12039867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12039920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12039923	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12040033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12040121	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12040237	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12040880	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12041108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12041180	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12041732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12041849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12042159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12043955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12044515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12044896	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12044901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12045663	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12045991	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12046726	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12047490	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12047951	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12048746	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12049068	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1603126	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17098662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17103209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17103224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17103273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17103305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103314	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103450	1.00[AMR][1000 genomes]
rs2088103	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2132054	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3000143	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3000144	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3000145	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3000146	0.96[ASN][1000 genomes]
rs3015018	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7525048	1.00[AMR][1000 genomes]
rs9425165	0.84[EUR][1000 genomes];0.96[ASN][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	nsv1004014	chr1:79811049-80042309	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1012004	chr1:79945395-80096748	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv535017	chr1:79945395-80096748	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1012296	chr1:79945395-80300216	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1005022	chr1:79950774-80106902	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv546636	chr1:79964823-80079996	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79983000-79985200	Enhancers	Primary T cells from cord blood	blood
2	chr1:79983200-79984600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:79983600-79984000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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