Variant report

Variant	rs12509054
Chromosome Location	chr4:120115075-120115076
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-455G16.1.1-3	chr4:120114843-120115546	NONHSAT098035

Extended variants
information (count: 95 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10006304	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10006877	0.85[CEU][hapmap]
rs10010696	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10013032	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10022508	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10029750	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10031033	0.88[MEX][hapmap];0.81[EUR][1000 genomes]
rs1011054	0.95[CEU][hapmap];0.88[LWK][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs10213342	0.80[EUR][1000 genomes]
rs1033087	0.92[ASN][1000 genomes]
rs11098490	0.88[ASN][1000 genomes]
rs11098491	0.88[ASN][1000 genomes]
rs11098492	0.91[ASN][1000 genomes]
rs11098493	0.92[ASN][1000 genomes]
rs11098496	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11098499	0.95[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs11726229	0.94[CEU][hapmap]
rs11729897	0.80[AMR][1000 genomes]
rs11733239	0.88[ASN][1000 genomes]
rs11931312	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11944880	0.95[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12186259	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12501610	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12502503	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12506395	0.81[EUR][1000 genomes]
rs12512517	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12513191	0.91[ASN][1000 genomes]
rs13113112	0.95[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13114751	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13120560	0.89[ASN][1000 genomes]
rs13123591	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13126596	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13129661	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs13136593	0.91[ASN][1000 genomes]
rs13138782	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13139045	0.85[CEU][hapmap]
rs13435802	0.85[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1397608	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1511015	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1511018	0.95[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1511019	0.95[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1511025	0.82[MEX][hapmap]
rs1546502	0.85[CEU][hapmap]
rs1546505	0.85[CEU][hapmap]
rs1551	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17839089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2036861	0.92[ASN][1000 genomes]
rs2203039	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28374891	0.81[EUR][1000 genomes]
rs28452522	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34585914	0.81[EUR][1000 genomes]
rs34616304	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34630083	0.80[AMR][1000 genomes]
rs35197422	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35271032	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35434465	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35643470	0.81[EUR][1000 genomes]
rs35916640	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3749591	0.95[CEU][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs4145951	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4355373	0.88[ASN][1000 genomes]
rs4833612	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4833613	0.87[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs56122576	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56386062	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6534130	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67073020	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs68128210	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6814412	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6815725	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6822498	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6826823	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6832670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6837898	0.95[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6838674	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6845702	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6849889	0.95[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs6851130	0.91[ASN][1000 genomes]
rs6851169	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7441137	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7659194	0.95[CEU][hapmap]
rs7661020	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7684942	0.85[EUR][1000 genomes]
rs7685268	0.86[EUR][1000 genomes]
rs951570	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9884728	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9993110	0.90[ASN][1000 genomes]
rs9995277	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9996382	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1008115	chr4:120007913-120143849	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv522386	chr4:120009147-120115379	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	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
6	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12509054	LOC284701///FLJ14186///LOC441124///LOC641693///LOC642788///LOC653056	cis	lesional skin	skin_eQTL
rs12509054	USP53	cis	cerebellum	SCAN
rs12509054	RP11-33B1.1	cis	Whole Blood	GTEx
rs12509054	RP11-384K6.6	cis	Whole Blood	GTEx
rs12509054	RP11-33B1.1	cis	lung	GTEx
rs12509054	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs12509054	RP11-33B1.1	cis	Nerve Tibial	GTEx
rs12509054	C4orf3	cis	cerebellum	SCAN
rs12509054	LOC284701///FLJ14186///LOC441124///LOC641693///LOC642788///LOC653056	cis	uninvolved skin	skin_eQTL
rs12509054	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120101000-120132400	Weak transcription	Left Ventricle	heart
2	chr4:120106200-120119200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:120112200-120116400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:120113000-120125200	Weak transcription	Right Atrium	heart

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