Variant report

Variant	rs2972415
Chromosome Location	chr5:42397082-42397083
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:42396008..42397874-chr5:42401912..42404104,2	K562	blood:

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10061299	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10755268	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1117110	0.91[EUR][1000 genomes]
rs11738365	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs11742495	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11747975	0.88[CEU][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748366	0.94[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11957616	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13162973	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1396768	0.95[EUR][1000 genomes]
rs1396773	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1467049	0.89[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509452	0.80[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509453	1.00[ASN][1000 genomes]
rs1509455	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1509456	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs1567374	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1605848	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1605851	0.91[EUR][1000 genomes]
rs1858136	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1858137	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1858139	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876788	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876790	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs1912107	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1960498	0.89[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs2036745	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs2175126	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2202883	0.90[EUR][1000 genomes]
rs2221712	0.90[EUR][1000 genomes]
rs2395970	0.91[EUR][1000 genomes]
rs2940912	0.98[EUR][1000 genomes]
rs2940914	0.91[EUR][1000 genomes]
rs2940916	1.00[CEU][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940917	0.89[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs2940918	0.89[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs2940919	0.89[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs2940920	0.89[CEU][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940922	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs2940926	0.89[CEU][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940928	0.81[EUR][1000 genomes]
rs2940929	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940931	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940934	0.91[EUR][1000 genomes]
rs2940935	0.80[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940939	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2940942	0.80[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940943	0.80[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972391	1.00[ASN][1000 genomes]
rs2972395	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972400	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972404	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972406	0.88[EUR][1000 genomes]
rs2972407	0.89[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs2972410	0.89[EUR][1000 genomes]
rs2972411	0.89[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs2972412	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs2972413	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs2972414	0.84[EUR][1000 genomes]
rs2972416	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs2972417	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972419	0.80[CEU][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34509769	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4642376	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4866890	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58416991	1.00[ASN][1000 genomes]
rs58960035	1.00[ASN][1000 genomes]
rs60126365	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61636452	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62370642	1.00[ASN][1000 genomes]
rs62370646	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62370648	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6451614	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6876736	0.91[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881436	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884737	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7379192	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704355	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728337	0.89[CEU][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9686286	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs974051	0.80[CEU][hapmap];0.90[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	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv881375	chr5:42254097-42442715	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv948514	chr5:42270161-42519262	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2972415	TTC33	cis	cerebellum	SCAN
rs2972415	GHR	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42396200-42397600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:42396800-42398000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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