Variant report

Variant	rs12623509
Chromosome Location	chr2:86818868-86818869
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86817719..86819365-chr2:86821480..86823766,2	K562	blood:
2	chr2:86788344..86791163-chr2:86817304..86820517,4	MCF-7	breast:
3	chr2:86815800..86817434-chr2:86817538..86820109,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115561	Chromatin interaction
ENSG00000228363	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1015117	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap]
rs10169746	0.83[ASN][1000 genomes]
rs10180036	0.89[CEU][hapmap]
rs10184584	0.83[ASN][1000 genomes]
rs10184879	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10184985	1.00[ASN][1000 genomes]
rs10187753	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10187880	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs10432704	0.81[ASN][1000 genomes]
rs1080551	0.83[ASN][1000 genomes]
rs11127045	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap]
rs11127047	1.00[CHD][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs11689330	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12328637	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12613282	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12614447	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap]
rs12615285	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap]
rs12714186	0.92[CEU][hapmap]
rs12714190	1.00[CHB][hapmap]
rs12714198	0.92[CEU][hapmap]
rs12714199	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs12987172	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12991654	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13015620	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13034615	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap]
rs1518807	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs1629293	1.00[CHB][hapmap];0.85[GIH][hapmap]
rs2241803	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap]
rs2292887	0.93[CEU][hapmap]
rs2367546	0.99[ASN][1000 genomes]
rs308902	0.80[GIH][hapmap]
rs308907	0.83[GIH][hapmap]
rs308910	0.83[GIH][hapmap]
rs308911	0.83[GIH][hapmap]
rs308914	0.85[GIH][hapmap]
rs3201448	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap]
rs34666164	0.83[ASN][1000 genomes]
rs3755002	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap]
rs422240	0.83[GIH][hapmap]
rs4240204	0.81[EUR][1000 genomes]
rs433655	0.83[GIH][hapmap]
rs4832042	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4832043	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4832297	0.96[CEU][hapmap]
rs4832300	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4832302	0.83[ASN][1000 genomes]
rs4832303	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4832304	0.96[CEU][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62147239	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6547700	0.89[GIH][hapmap]
rs6728211	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6733569	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6738663	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6750226	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6752371	1.00[CHB][hapmap];0.80[GIH][hapmap];0.81[ASN][1000 genomes]
rs7557796	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs7568840	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7570640	0.83[ASN][1000 genomes]
rs7584882	1.00[CHB][hapmap];0.80[GIH][hapmap];0.81[ASN][1000 genomes]
rs7587034	0.83[ASN][1000 genomes]
rs7596717	1.00[CHB][hapmap]
rs7601115	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9284788	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap]
rs958561	0.93[CEU][hapmap]
rs966477	0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv818064	chr2:86818868-86819409	Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12623509	POLR1A	cis	cerebellum	SCAN
rs12623509	IMMT	cis	parietal	SCAN
rs12623509	VPS24	Cis_1M	lymphoblastoid	RTeQTL

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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