Variant report

Variant	rs12665409
Chromosome Location	chr6:118685043-118685044
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10456917	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10457330	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10457331	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10457335	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10457337	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10457338	1.00[CEU][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11153732	0.86[EUR][1000 genomes]
rs11153734	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11153748	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11153752	1.00[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11153753	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11753128	0.84[EUR][1000 genomes]
rs11755121	1.00[CEU][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11970286	0.90[ASN][1000 genomes]
rs12192682	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12192964	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12194555	1.00[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12197337	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12198461	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12199463	1.00[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12205899	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12206329	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12207209	0.84[EUR][1000 genomes]
rs12211576	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12214483	1.00[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12660455	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13192336	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13192574	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13217710	0.85[EUR][1000 genomes]
rs13219555	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2077162	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2213856	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2213857	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2356183	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2356492	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28655926	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34479834	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35730412	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3734381	0.85[EUR][1000 genomes]
rs3752581	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3798420	1.00[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3890198	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3951042	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3951043	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs397445	0.88[CEU][hapmap]
rs4027880	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs419592	0.88[CEU][hapmap]
rs4307206	0.95[MEX][hapmap]
rs445566	0.85[CEU][hapmap]
rs4946347	0.82[EUR][1000 genomes]
rs56403768	0.81[ASN][1000 genomes]
rs57813349	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57912492	0.81[ASN][1000 genomes]
rs6569013	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6569014	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569015	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569020	0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67832971	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6903459	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6920640	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6925641	1.00[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6928210	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6936178	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6938041	0.85[EUR][1000 genomes]
rs6938226	0.84[EUR][1000 genomes]
rs7453914	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7746778	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7751467	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7757892	0.85[EUR][1000 genomes]
rs7757943	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7758614	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7764272	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7764280	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7767864	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7772214	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9320648	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9320649	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9489355	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs973944	0.96[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530526	chr6:118027339-118718476	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv532051	chr6:118551027-119044197	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1020463	chr6:118593028-119146363	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv604554	chr6:118631282-118716318	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv830787	chr6:118631902-118805106	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1025403	chr6:118635123-119122551	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1025456	chr6:118669672-119058789	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12665409	C6orf204	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118680200-118689400	Weak transcription	Psoas Muscle	Psoas

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