Variant report

Variant	rs6582392
Chromosome Location	chr12:42640396-42640397
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:42631376..42634368-chr12:42640313..42643094,3	MCF-7	breast:
2	chr12:42630899..42632760-chr12:42639742..42641533,2	K562	blood:
3	chr12:42629596..42634057-chr12:42635851..42641617,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134283	Chromatin interaction
ENSG00000015153	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1069644	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10785335	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10785337	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10880275	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880280	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10880282	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10880284	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.81[EUR][1000 genomes]
rs11181461	0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap]
rs1118483	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226298	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1226303	0.88[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap]
rs1238290	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12423383	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.81[EUR][1000 genomes]
rs12425945	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs12578312	0.92[CEU][hapmap]
rs1376931	0.92[CEU][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs1463613	0.93[JPT][hapmap]
rs1628871	0.92[JPT][hapmap]
rs1669903	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap]
rs1669937	0.92[CEU][hapmap]
rs1683195	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17091052	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1732351	0.82[GIH][hapmap];0.87[JPT][hapmap]
rs1732352	0.87[JPT][hapmap]
rs1796357	0.92[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs1796389	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap]
rs1796398	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs1826387	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1961953	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2061191	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2061192	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2085314	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2100547	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2198763	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2243465	0.92[CEU][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs2605401	0.86[CEU][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3761677	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.81[EUR][1000 genomes]
rs3827524	0.92[CEU][hapmap];0.90[CHB][hapmap]
rs4402364	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4417370	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768397	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs4768398	0.96[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4768401	0.92[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs6582378	0.83[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap]
rs6582385	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6582386	0.86[EUR][1000 genomes]
rs6582389	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs712106	0.93[JPT][hapmap]
rs712108	0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712109	0.88[CEU][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs712112	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs712114	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712115	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712118	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs712119	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.91[YRI][hapmap]
rs712120	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs712122	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712123	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712125	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712126	0.88[CEU][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs712127	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs712129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7134895	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7298965	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7302687	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7303028	0.82[GIH][hapmap]
rs7316575	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7486516	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7956016	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7959339	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7960176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970115	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7975518	0.88[CEU][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7978993	0.87[JPT][hapmap];0.85[LWK][hapmap];0.82[YRI][hapmap]
rs824716	0.87[JPT][hapmap]
rs824724	0.87[JPT][hapmap]
rs824734	0.88[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap]
rs824738	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs824739	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs824741	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs824742	0.81[EUR][1000 genomes]
rs844046	0.93[JPT][hapmap]
rs865420	0.88[CHD][hapmap];0.93[JPT][hapmap]
rs866091	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs896555	0.92[CEU][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]

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	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv826351	chr12:42584218-42676281	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv826352	chr12:42593124-42675255	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv3397788	chr12:42636734-42665519	Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6582392	PPHLN1	cis	Artery Tibial	GTEx
rs6582392	PPHLN1	cis	multi-tissue	Pritchard
rs6582392	MADP-1	cis	multi-tissue	Pritchard

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

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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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