Variant report

Variant	rs17009144
Chromosome Location	chr4:120270795-120270796
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 125 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10000544	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10003567	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs10006192	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10006259	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs10006525	0.81[TSI][hapmap]
rs10006688	0.81[AMR][1000 genomes]
rs10006706	0.81[TSI][hapmap]
rs10009626	0.81[CHB][hapmap]
rs10012408	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10013032	0.81[CEU][hapmap]
rs10013042	0.90[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs10015579	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10015965	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10016241	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10017335	0.81[TSI][hapmap]
rs10022448	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10023641	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10025925	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10028773	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10029303	0.84[ASN][1000 genomes]
rs10031033	0.81[CEU][hapmap]
rs10434028	0.83[ASN][1000 genomes]
rs10517834	0.80[ASN][1000 genomes]
rs10518300	0.94[ASW][hapmap];0.90[CEU][hapmap];0.83[CHD][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap]
rs10518328	0.81[TSI][hapmap]
rs10518329	0.81[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap]
rs10857066	0.82[ASN][1000 genomes]
rs11098501	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs11098506	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs11098507	0.84[ASN][1000 genomes]
rs1155577	0.84[CHD][hapmap]
rs11729521	0.81[TSI][hapmap]
rs11732686	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs11734241	0.81[TSI][hapmap]
rs12374396	0.81[ASN][1000 genomes]
rs12498657	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12502393	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12502423	0.81[TSI][hapmap]
rs12502524	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12503082	0.84[ASN][1000 genomes]
rs12506421	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12506445	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12506487	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12507565	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs12508504	0.81[TSI][hapmap]
rs12510133	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12510138	0.81[TSI][hapmap]
rs12511640	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs12513083	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs12513310	0.81[ASN][1000 genomes]
rs12711071	1.00[ASW][hapmap];0.90[CEU][hapmap];0.82[CHD][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs13104219	0.81[CHB][hapmap]
rs13125526	0.80[ASN][1000 genomes]
rs13134517	0.81[CHB][hapmap]
rs13139045	0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap]
rs1480931	0.81[TSI][hapmap]
rs1480933	0.84[CHD][hapmap]
rs1511017	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs1511025	1.00[ASW][hapmap];0.90[CEU][hapmap];0.83[CHD][hapmap];0.98[LWK][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap]
rs1546503	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs1546505	0.81[CHD][hapmap];0.88[TSI][hapmap]
rs1814813	0.84[AMR][1000 genomes]
rs1814814	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1980025	0.94[ASW][hapmap];0.90[CEU][hapmap];0.82[CHD][hapmap];0.98[LWK][hapmap];0.80[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs1980026	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs2136911	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2203039	0.81[CEU][hapmap]
rs2389803	0.81[TSI][hapmap]
rs28369518	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28396837	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28437684	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28470894	0.82[ASN][1000 genomes]
rs28502463	0.81[AFR][1000 genomes]
rs28546691	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28551750	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28572003	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28581362	0.85[ASN][1000 genomes]
rs28589345	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28594160	0.86[ASN][1000 genomes]
rs28599836	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28691602	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28714087	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28726222	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3733524	0.81[TSI][hapmap]
rs3864142	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3864144	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4001390	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4422403	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs55820750	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55845118	0.82[ASN][1000 genomes]
rs60378962	0.80[ASN][1000 genomes]
rs6534130	0.81[CEU][hapmap]
rs67281037	0.81[ASN][1000 genomes]
rs6815291	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6824111	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs6834796	0.81[TSI][hapmap]
rs6838009	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6838457	0.86[AMR][1000 genomes]
rs6843229	0.81[CHB][hapmap]
rs6847586	0.80[ASN][1000 genomes]
rs6847862	0.85[ASN][1000 genomes]
rs6848081	0.82[ASN][1000 genomes]
rs6848380	0.85[ASN][1000 genomes]
rs6848389	0.81[TSI][hapmap]
rs6849561	0.81[TSI][hapmap]
rs714899	0.90[CEU][hapmap];0.89[YRI][hapmap]
rs72676059	0.82[ASN][1000 genomes]
rs7665125	0.81[CEU][hapmap];0.95[CHB][hapmap]
rs7672594	1.00[ASW][hapmap];0.90[CEU][hapmap];0.83[CHD][hapmap];0.98[LWK][hapmap];0.80[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs7692994	0.81[CEU][hapmap];0.90[CHB][hapmap]
rs878372	1.00[ASW][hapmap];0.90[CEU][hapmap];0.83[CHD][hapmap];0.98[LWK][hapmap];0.80[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs907205	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs9991959	1.00[ASW][hapmap];0.90[CEU][hapmap];0.83[CHD][hapmap];0.98[LWK][hapmap];0.80[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs9995136	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs9995716	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9999724	0.90[CEU][hapmap];0.82[CHD][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv428769	chr4:120205572-120363323	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv879841	chr4:120244085-120388406	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv879842	chr4:120244085-120424087	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv427694	chr4:120250511-120501728	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv2538163	chr4:120252854-120388678	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv964091	chr4:120255342-120290951	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs17009144	RP11-33B1.1	cis	Esophagus Mucosa	GTEx
rs17009144	RP11-384K6.6	cis	Whole Blood	GTEx
rs17009144	SYNPO2	cis	cerebellum	SCAN
rs17009144	RP11-33B1.1	cis	lung	GTEx
rs17009144	USP53	cis	cerebellum	SCAN
rs17009144	RP11-33B1.1	cis	Nerve Tibial	GTEx
rs17009144	LOC284701///FLJ14186///LOC441124///LOC641693///LOC642788///LOC653056	cis	uninvolved skin	skin_eQTL
rs17009144	RP11-33B1.1	cis	Whole Blood	GTEx
rs17009144	LOC644243	trans	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120266400-120275000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr4:120269200-120277600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr4:120269600-120293000	Weak transcription	Fetal Heart	heart

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