Variant report

Variant	rs6573009
Chromosome Location	chr14:55682324-55682325
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	chr14:55678554..55682853-chr14:55737022..55740091,3	K562	blood:

Variant related genes	Relation type
ENSG00000178974	Chromatin interaction
ENSG00000258413	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs1009977	0.81[CEU][hapmap];0.92[TSI][hapmap]
rs1009978	0.84[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes]
rs10131913	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10131926	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10134339	0.87[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap]
rs10134800	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10136596	0.96[CEU][hapmap]
rs10137307	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs10138446	0.85[MEX][hapmap]
rs10139083	0.86[EUR][1000 genomes]
rs10139337	0.85[EUR][1000 genomes]
rs10139678	0.85[EUR][1000 genomes]
rs10140801	0.89[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10140869	0.92[CEU][hapmap]
rs10141483	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10141552	0.96[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs10142448	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs10142547	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10142823	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10144345	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10144418	0.92[CEU][hapmap];0.82[TSI][hapmap]
rs10145203	0.84[EUR][1000 genomes]
rs10147667	0.85[CEU][hapmap]
rs10149420	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10150699	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10150760	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs1045002	0.96[CEU][hapmap]
rs10467798	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1109170	0.87[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11547116	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11622740	0.81[CEU][hapmap]
rs11625001	1.00[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs11625423	0.83[EUR][1000 genomes]
rs11625968	0.95[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap]
rs11628437	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11851169	1.00[CEU][hapmap]
rs12050099	0.84[EUR][1000 genomes]
rs13379169	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1538257	0.85[MEX][hapmap]
rs1572611	0.85[CEU][hapmap]
rs17128183	0.84[AMR][1000 genomes]
rs17674463	0.96[CEU][hapmap]
rs17740741	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs17741542	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs17741831	0.96[CEU][hapmap]
rs1815581	0.82[AMR][1000 genomes]
rs1952087	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2009291	0.87[ASW][hapmap];0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes]
rs2075601	1.00[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2075602	1.00[ASW][hapmap];0.92[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2075603	0.81[CEU][hapmap]
rs2147964	1.00[YRI][hapmap]
rs2274273	0.81[CEU][hapmap];0.87[TSI][hapmap]
rs2340921	1.00[YRI][hapmap]
rs2340931	0.85[CEU][hapmap];0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2341621	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2341622	0.87[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28429419	0.84[AMR][1000 genomes]
rs28568813	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28631821	0.81[AMR][1000 genomes]
rs28716725	0.83[AFR][1000 genomes]
rs3742569	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs3783650	0.87[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3783651	0.81[JPT][hapmap]
rs3783652	1.00[CEU][hapmap]
rs3818451	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3825613	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs3825616	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4366639	0.83[EUR][1000 genomes]
rs4496026	0.83[EUR][1000 genomes]
rs4519260	0.83[AMR][1000 genomes]
rs4597235	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4644	0.85[TSI][hapmap]
rs4652	0.88[ASW][hapmap];0.88[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs56660630	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56949365	0.83[EUR][1000 genomes]
rs58260073	0.87[EUR][1000 genomes]
rs59629906	0.85[EUR][1000 genomes]
rs59871474	0.85[EUR][1000 genomes]
rs60248556	0.87[EUR][1000 genomes]
rs61210954	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6573007	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6573010	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6573012	0.85[AMR][1000 genomes]
rs6573013	0.87[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs6573014	0.87[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6573017	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs6573020	0.96[CEU][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap]
rs66696758	0.87[EUR][1000 genomes]
rs67514154	0.86[EUR][1000 genomes]
rs68046603	0.85[EUR][1000 genomes]
rs7142857	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7144292	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7144737	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs7146748	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7146752	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7147106	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7148171	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7153110	0.87[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap]
rs7153612	0.84[EUR][1000 genomes]
rs7153645	0.87[EUR][1000 genomes]
rs7154889	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs7158768	0.87[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7159144	0.96[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs7159808	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7160110	0.81[CEU][hapmap];0.92[TSI][hapmap]
rs7160523	1.00[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72715769	0.88[EUR][1000 genomes]
rs8004787	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8006525	0.96[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs8007614	0.92[CEU][hapmap];0.82[TSI][hapmap]
rs8007620	0.92[CEU][hapmap]
rs8007944	0.84[AMR][1000 genomes]
rs8009670	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs8011288	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8013027	0.85[CEU][hapmap]
rs8013713	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs8018110	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8019978	1.00[YRI][hapmap]
rs8021583	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs8022225	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8023197	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs9323284	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs943590	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs946059	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9919926	0.89[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035158	chr14:55638386-55684228	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6573009	RP11-665C16.6	cis	Muscle Skeletal	GTEx
rs6573009	FBXO34	cis	multi-tissue	Pritchard
rs6573009	FBXO34	cis	cerebellum	SCAN
rs6573009	WDHD1	cis	parietal	SCAN
rs6573009	ATG14	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55679800-55684800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr14:55679800-55685200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr14:55679800-55685200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr14:55680200-55685600	Weak transcription	NHEK	skin
5	chr14:55680400-55685000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr14:55680400-55685000	Weak transcription	HMEC	breast

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