Variant report

Variant	rs6574055
Chromosome Location	chr14:72702497-72702498
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:72576115..72579038-chr14:72700345..72702644,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10131012	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10134489	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10134542	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10143449	0.81[ASN][1000 genomes]
rs10149098	0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10150159	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10150242	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1076317	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs11848300	0.86[JPT][hapmap];0.87[MEX][hapmap]
rs12148024	0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs12432346	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[ASN][1000 genomes]
rs12432632	0.90[ASN][1000 genomes]
rs12894979	0.91[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs1402056	0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs1402058	0.86[JPT][hapmap]
rs1402061	0.86[JPT][hapmap]
rs1520326	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1544487	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1558071	0.82[ASN][1000 genomes]
rs1558073	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1568404	0.81[JPT][hapmap]
rs17180251	0.82[ASN][1000 genomes]
rs1949560	0.83[MEX][hapmap]
rs2079502	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2108466	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2158988	0.82[TSI][hapmap]
rs2238212	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2238213	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2238215	0.91[JPT][hapmap]
rs2238216	0.91[JPT][hapmap]
rs2238217	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2238218	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2238243	0.91[JPT][hapmap]
rs2238244	0.91[JPT][hapmap]
rs2239257	0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2239258	1.00[JPT][hapmap]
rs2239261	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2283407	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2283408	0.86[JPT][hapmap]
rs2332806	0.86[JPT][hapmap]
rs2332807	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs2332808	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3784049	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4903003	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs4903004	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6574054	0.80[MEX][hapmap]
rs6574056	0.94[ASN][1000 genomes]
rs6574057	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs699369	0.84[ASN][1000 genomes]
rs7157673	0.82[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7350728	0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs740337	0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs763507	0.91[JPT][hapmap]
rs8007566	0.82[JPT][hapmap]
rs8007922	0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs847241	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs847304	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs847308	0.84[TSI][hapmap]
rs847345	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs977340	0.82[MEX][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	nsv530794	chr14:72113818-73034008	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv948800	chr14:72462557-73150701	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1041492	chr14:72634606-72768970	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv977614	chr14:72696106-72702781	Weak transcription Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6574055	VTI1B	cis	cerebellum	SCAN
rs6574055	COX16	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72687800-72705800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr14:72699800-72719600	Weak transcription	Right Ventricle	heart
3	chr14:72700600-72709800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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