Variant report

Variant	rs12039386
Chromosome Location	chr1:212676661-212676662
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212661275..212664884-chr1:212673911..212677045,3	K562	blood:
2	chr1:212676521..212678567-chr1:212731276..212732925,2	K562	blood:
3	chr1:212675839..212678567-chr1:212731045..212732925,2	K562	blood:
4	chr1:212675568..212680156-chr1:212685148..212688870,4	K562	blood:
5	chr1:212673623..212675813-chr1:212676044..212678475,3	K562	blood:
6	chr1:212675043..212677212-chr1:212781666..212783527,2	K562	blood:

Variant related genes	Relation type
ENSG00000260805	Chromatin interaction
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10863970	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10863971	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10863972	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10863975	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10863978	0.85[ASN][1000 genomes]
rs11119949	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119950	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119951	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11119953	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11119956	0.85[ASN][1000 genomes]
rs12030310	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12046220	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12049168	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12143427	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12410743	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12568048	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12569340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1807387	1.00[AFR][1000 genomes]
rs1965301	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4347269	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4951602	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951603	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951606	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4951607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72649983	1.00[AFR][1000 genomes]
rs72649985	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72649986	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72649987	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72649988	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72649989	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72649990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72649991	0.85[ASN][1000 genomes]
rs750227	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs750228	0.92[ASN][1000 genomes]
rs8179354	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
5	nsv873161	chr1:212610755-212683565	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv873162	chr1:212610755-212716033	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv527863	chr1:212617423-212700618	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
9	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212663200-212678400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:212667200-212686400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:212670000-212679800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:212672000-212679800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:212672000-212680000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:212672200-212680600	Weak transcription	Right Atrium	heart
7	chr1:212673000-212680000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:212675400-212676800	Enhancers	GM12878-XiMat	blood
9	chr1:212675600-212676800	Enhancers	HMEC	breast
10	chr1:212675800-212677400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:212675800-212680600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:212676000-212677200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:212676000-212679600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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