Variant report

Variant	rs17825393
Chromosome Location	chr6:118772583-118772584
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLN-2	chr6:118772307-118773627	NONHSAT114692

Extended variants
information (count: 131 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10456917	0.94[ASN][1000 genomes]
rs10457330	0.92[ASN][1000 genomes]
rs10457331	0.92[ASN][1000 genomes]
rs10457335	0.94[ASN][1000 genomes]
rs10457337	0.93[ASN][1000 genomes]
rs10457338	0.94[CHB][hapmap];0.94[ASN][1000 genomes]
rs10457342	0.80[ASN][1000 genomes]
rs11153730	0.81[EUR][1000 genomes]
rs11153732	0.89[ASN][1000 genomes]
rs11153734	0.92[ASN][1000 genomes]
rs11153748	0.94[ASN][1000 genomes]
rs11153752	0.94[CHB][hapmap];0.89[ASN][1000 genomes]
rs11153753	0.88[ASN][1000 genomes]
rs11153759	0.82[ASN][1000 genomes]
rs11153763	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs11153767	0.80[ASN][1000 genomes]
rs11752626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11752928	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11753128	0.89[ASN][1000 genomes]
rs11755121	0.88[CHB][hapmap];0.89[ASN][1000 genomes]
rs11758454	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11965985	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11967375	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11967858	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11968176	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11968351	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs11970286	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12192682	0.85[ASN][1000 genomes]
rs12192964	0.92[ASN][1000 genomes]
rs12194555	0.94[CHB][hapmap];0.95[MEX][hapmap];0.89[ASN][1000 genomes]
rs12197337	0.84[ASN][1000 genomes]
rs12198461	0.83[ASN][1000 genomes]
rs12199463	0.94[CHB][hapmap];0.85[MEX][hapmap];0.89[ASN][1000 genomes]
rs12203006	0.82[ASN][1000 genomes]
rs12206329	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs12207209	0.89[ASN][1000 genomes]
rs12208253	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs12211576	0.85[ASN][1000 genomes]
rs12214483	0.94[CHB][hapmap];0.94[ASN][1000 genomes]
rs12660455	0.92[ASN][1000 genomes]
rs12661338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13191610	0.82[ASN][1000 genomes]
rs13192336	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs13192574	0.85[ASN][1000 genomes]
rs13217710	0.86[ASN][1000 genomes]
rs13219555	0.90[ASN][1000 genomes]
rs13220480	0.94[CHB][hapmap];0.95[MEX][hapmap];0.82[ASN][1000 genomes]
rs1572226	0.84[MEX][hapmap]
rs17226667	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17227124	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17825652	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2078079	0.87[ASN][1000 genomes]
rs2078383	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2184402	0.83[ASN][1000 genomes]
rs2213856	0.94[CHB][hapmap];0.93[ASN][1000 genomes]
rs2213857	0.92[ASN][1000 genomes]
rs2356183	0.94[ASN][1000 genomes]
rs2356492	0.94[CHB][hapmap];0.92[ASN][1000 genomes]
rs2356497	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2356498	0.82[ASN][1000 genomes]
rs2883956	0.82[ASN][1000 genomes]
rs34479834	0.89[ASN][1000 genomes]
rs35029749	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35730412	0.91[ASN][1000 genomes]
rs35962656	0.82[ASN][1000 genomes]
rs3734381	0.81[CHB][hapmap];0.89[MEX][hapmap]
rs3752581	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs3798420	0.94[CHB][hapmap];0.94[MEX][hapmap];0.94[ASN][1000 genomes]
rs3890198	0.91[ASN][1000 genomes]
rs3951042	0.92[ASN][1000 genomes]
rs3951043	0.92[ASN][1000 genomes]
rs4027880	0.92[ASN][1000 genomes]
rs4307206	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4945623	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4946347	0.89[ASN][1000 genomes]
rs4946350	0.82[ASN][1000 genomes]
rs56403768	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57813349	0.92[ASN][1000 genomes]
rs57912492	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59671368	0.82[ASN][1000 genomes]
rs6569020	0.93[CHB][hapmap];0.92[ASN][1000 genomes]
rs6569024	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67832971	0.89[ASN][1000 genomes]
rs6902812	0.93[CHB][hapmap];0.83[ASN][1000 genomes]
rs6906287	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6925641	0.94[CHB][hapmap];0.95[MEX][hapmap];0.89[ASN][1000 genomes]
rs6936178	0.92[ASN][1000 genomes]
rs6938041	0.89[ASN][1000 genomes]
rs6938226	0.89[ASN][1000 genomes]
rs72952771	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72952795	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72958930	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72967533	0.80[EUR][1000 genomes]
rs763254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7740645	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs7746778	0.90[ASN][1000 genomes]
rs7751467	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs7757892	0.88[ASN][1000 genomes]
rs7758614	0.82[ASN][1000 genomes]
rs7763596	0.82[ASN][1000 genomes]
rs7766375	0.80[ASN][1000 genomes]
rs7769001	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs7772214	0.91[ASN][1000 genomes]
rs7772921	0.80[ASN][1000 genomes]
rs7773274	0.83[ASN][1000 genomes]
rs973944	0.94[CHB][hapmap];0.94[MEX][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv1027444	chr6:118687556-119121660	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv538428	chr6:118687556-119121660	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv949321	chr6:118692304-119137658	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv432958	chr6:118692307-119010307	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv604555	chr6:118695049-118856822	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv1034448	chr6:118698169-119016383	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	nsv1025097	chr6:118699752-119058789	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
13	nsv1020586	chr6:118711098-118900012	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
14	nsv532052	chr6:118711850-119057295	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' 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
15	nsv432959	chr6:118716318-119010307	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers 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	9 gene(s)	inside rSNPs	diseases
16	nsv604556	chr6:118722589-119065365	Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
17	nsv432960	chr6:118723307-118826307	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
18	nsv525179	chr6:118726243-118876092	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
19	nsv1019357	chr6:118731468-118860705	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
20	nsv464027	chr6:118768150-118856822	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a
21	nsv604557	chr6:118768150-118856822	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a
22	nsv464029	chr6:118768150-118861263	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a
23	nsv604558	chr6:118768150-118861263	Weak transcription Genic enhancers ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a
24	nsv949416	chr6:118772508-119033063	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
25	nsv948980	chr6:118772508-119137658	Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17825393	C6orf204	cis	cerebellum	SCAN
rs17825393	SLC35F1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118763600-118772600	Weak transcription	Muscle Satellite Cultured Cells	--

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