Variant report

Variant	rs10144448
Chromosome Location	chr14:78233912-78233913
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	chr14:78225206..78227970-chr14:78231948..78234705,2	MCF-7	breast:
2	chr14:78227646..78229706-chr14:78233866..78236493,2	K562	blood:

Variant related genes	Relation type
ENSG00000268208	Chromatin interaction
ENSG00000100603	Chromatin interaction
ENSG00000197734	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1006038	0.90[CHB][hapmap]
rs1006039	0.90[CHB][hapmap]
rs1006040	0.90[CHB][hapmap]
rs1008988	0.95[CHB][hapmap]
rs10134425	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10138747	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10139492	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10142722	0.90[CHB][hapmap]
rs10143249	0.84[ASN][1000 genomes]
rs10143294	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10146255	0.98[ASN][1000 genomes]
rs1048147	0.90[CHB][hapmap]
rs10483885	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs114763	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs11621719	0.83[ASN][1000 genomes]
rs11622761	0.83[ASN][1000 genomes]
rs11624118	0.83[ASN][1000 genomes]
rs11628888	0.85[CHB][hapmap]
rs11846215	0.91[ASN][1000 genomes]
rs12879880	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12885306	1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap]
rs12887313	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12890728	0.85[CHB][hapmap]
rs12890828	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1477262	0.90[CHB][hapmap]
rs1477263	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1477264	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17106157	0.90[CHB][hapmap]
rs176941	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs176943	0.90[CHB][hapmap]
rs176946	0.90[CHB][hapmap]
rs176947	0.87[ASN][1000 genomes]
rs176948	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs176951	0.90[CHB][hapmap]
rs176954	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs176955	0.90[CHB][hapmap]
rs176956	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs176959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs176961	0.93[ASN][1000 genomes]
rs176963	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176964	0.90[CHB][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176965	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176968	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176969	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176970	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176972	0.92[ASN][1000 genomes]
rs176975	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176976	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176977	0.90[ASN][1000 genomes]
rs176980	0.90[CHB][hapmap]
rs2080703	0.87[ASN][1000 genomes]
rs2267756	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2267759	0.90[CHB][hapmap]
rs2267760	0.90[CHB][hapmap]
rs2267761	0.90[CHB][hapmap]
rs2267762	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2267763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2267764	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2267766	0.82[AMR][1000 genomes]
rs2277917	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2284233	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2284234	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2284235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2299930	0.90[CHB][hapmap]
rs3759728	0.90[CHB][hapmap]
rs3783980	0.90[CHB][hapmap]
rs3783981	0.87[ASN][1000 genomes]
rs3783982	0.87[ASN][1000 genomes]
rs4632066	0.90[CHB][hapmap]
rs4641655	0.98[ASN][1000 genomes]
rs4899670	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4899673	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs4899674	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4903638	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61992867	0.80[ASN][1000 genomes]
rs61992868	0.80[ASN][1000 genomes]
rs6574392	0.97[ASN][1000 genomes]
rs6574394	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6574399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6574404	0.86[CHB][hapmap]
rs7142390	0.90[CHB][hapmap]
rs7143926	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7145717	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7148078	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs7148126	0.87[ASN][1000 genomes]
rs7150531	0.96[ASN][1000 genomes]
rs7151685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7154571	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7159310	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7160355	0.96[ASN][1000 genomes]
rs717682	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs759713	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs8003691	0.90[CHB][hapmap]
rs8010541	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8011337	0.90[CHB][hapmap]
rs8015645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8016447	0.90[CHB][hapmap]
rs8022516	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9323649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9323650	0.90[CHB][hapmap]
rs9323651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10144448	NEK9	cis	parietal	SCAN
rs10144448	ALDH6A1	cis	parietal	SCAN
rs10144448	RPS6KL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78228400-78234800	Weak transcription	Stomach Smooth Muscle	stomach

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