Variant report

Variant	rs4320988
Chromosome Location	chr12:39891473-39891474
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:39836009..39838675-chr12:39889597..39892071,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139116	Chromatin interaction
ENSG00000252974	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10876868	0.95[JPT][hapmap]
rs10876876	0.95[JPT][hapmap]
rs10876886	0.96[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs10876972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10877100	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11171720	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs11171789	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs11171891	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs11171901	0.86[CEU][hapmap];0.94[JPT][hapmap]
rs11171923	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11171938	0.84[CEU][hapmap]
rs11172108	0.96[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[EUR][1000 genomes]
rs11172120	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11172174	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11172183	0.82[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs11172264	0.80[ASN][1000 genomes]
rs11172282	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11172293	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11172319	0.90[ASN][1000 genomes]
rs11172320	0.87[ASN][1000 genomes]
rs11172357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172386	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172392	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172492	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172493	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172526	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11172541	0.87[ASN][1000 genomes]
rs11172592	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11172625	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11172638	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172650	0.85[ASN][1000 genomes]
rs11172661	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11830643	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs11836755	0.95[JPT][hapmap]
rs12228767	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs12230604	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs12424345	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs1512936	1.00[JPT][hapmap];0.93[YRI][hapmap]
rs1567739	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1828653	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs2388320	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3736466	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs4284427	0.91[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4378431	0.91[ASN][1000 genomes]
rs4390378	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4451772	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4466883	0.83[ASN][1000 genomes]
rs4475956	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4492858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4500523	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58240943	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58613501	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60263267	0.87[ASN][1000 genomes]
rs6581187	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6581188	0.84[ASN][1000 genomes]
rs7133376	0.92[YRI][hapmap]
rs7137143	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs73094410	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73096532	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7316073	0.92[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7485730	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7962283	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7964447	0.96[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs7965222	0.81[EUR][1000 genomes]
rs7966540	0.85[ASN][1000 genomes]
rs7968837	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7974928	0.84[CEU][hapmap]
rs7979444	0.88[CEU][hapmap];0.95[JPT][hapmap]

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	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1044049	chr12:39845078-39922808	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1051709	chr12:39846990-39899051	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1048933	chr12:39886665-39946270	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv975479	chr12:39890961-39892398	Inactive region	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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