Variant report

Variant	rs4632066
Chromosome Location	chr14:78247282-78247283
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:78227502..78229042-chr14:78246009..78248250,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268208	Chromatin interaction
ENSG00000100603	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1006038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1006039	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1006040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1008988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1008989	0.92[ASW][hapmap];0.81[LWK][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs10136053	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10139492	0.90[CHB][hapmap]
rs10142722	0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10143294	0.90[CHB][hapmap]
rs10144448	0.90[CHB][hapmap]
rs10148373	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10149619	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1048147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10483885	0.90[CHB][hapmap]
rs11159288	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs114763	0.90[CHB][hapmap]
rs11622565	0.83[ASN][1000 genomes]
rs11623088	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11624101	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11628888	0.93[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11847025	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12435761	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12883228	0.86[ASN][1000 genomes]
rs12885306	0.90[CHB][hapmap]
rs12887282	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12887606	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12890375	0.89[ASN][1000 genomes]
rs12890728	0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[ASN][1000 genomes]
rs13379065	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1469018	0.89[ASN][1000 genomes]
rs1477259	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1477260	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1477261	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1477262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1477264	0.90[CHB][hapmap]
rs1549119	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17106157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs176941	0.90[CHB][hapmap]
rs176943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs176944	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs176946	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs176951	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs176952	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs176953	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs176955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs176956	0.90[CHB][hapmap]
rs176957	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs176959	0.90[CHB][hapmap]
rs176960	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs176962	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs176963	0.90[CHB][hapmap]
rs176964	1.00[CHB][hapmap]
rs176965	0.90[CHB][hapmap]
rs176966	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs176971	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs176973	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs176979	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs176980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1978416	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1984925	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2032781	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2112136	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267756	0.90[CHB][hapmap]
rs2267758	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2267759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2267760	0.92[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2267761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2267762	0.90[CHB][hapmap]
rs2267763	0.90[CHB][hapmap]
rs2267764	0.90[CHB][hapmap]
rs2267767	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2267768	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2277917	0.90[CHB][hapmap]
rs2284234	0.90[CHB][hapmap]
rs2284235	0.90[CHB][hapmap]
rs2299930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2364584	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2364840	0.87[ASN][1000 genomes]
rs2544567	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28534379	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28603114	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35204328	0.84[ASN][1000 genomes]
rs3759728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3783980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3783983	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4383070	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4635269	0.82[ASN][1000 genomes]
rs4899670	0.90[CHB][hapmap]
rs4899673	0.90[CHB][hapmap]
rs4903643	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55909252	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56017708	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56412551	0.84[ASN][1000 genomes]
rs57635466	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61993668	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6574388	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6574391	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6574399	0.90[CHB][hapmap]
rs6574402	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6574404	0.95[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs7142390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7143926	0.90[CHB][hapmap]
rs7147516	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7148078	0.86[CHB][hapmap]
rs7151211	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7151685	0.90[CHB][hapmap]
rs7158826	0.81[ASN][1000 genomes]
rs717683	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72685264	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs759713	0.90[CHB][hapmap]
rs759808	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8003691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8003979	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8011337	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8014635	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8015645	0.90[CHB][hapmap]
rs8016175	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8016447	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8018741	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8018971	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9323649	0.90[CHB][hapmap]
rs9323650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap]
rs9323651	0.90[CHB][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	esv2758362	chr14:78074180-78262572	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv2759998	chr14:78074180-78262572	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1043788	chr14:78178490-78381190	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	esv2754594	chr14:78222798-78275549	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4632066	POMT2	cis	cerebellum	SCAN
rs4632066	ALKBH	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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