Variant report

Variant	rs715165
Chromosome Location	chr6:4100540-4100541
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf201-4	chr6:4100199-4101281	NONHSAT107311
2	lnc-C6orf201-4	chr6:4100111-4101281	NONHSAT107312
3	lnc-C6orf201-4	chr6:4100199-4101281	NONHSAT107310

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10085196	0.90[EUR][1000 genomes]
rs11759470	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[AMR][1000 genomes]
rs13196680	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[AMR][1000 genomes]
rs13197380	0.87[CEU][hapmap]
rs13200044	0.87[CEU][hapmap];0.81[AMR][1000 genomes]
rs13200786	0.81[AMR][1000 genomes]
rs13203009	0.81[AMR][1000 genomes]
rs13205642	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[EUR][1000 genomes]
rs13206444	0.90[EUR][1000 genomes]
rs13209389	0.87[CEU][hapmap];1.00[CHD][hapmap];0.81[AMR][1000 genomes]
rs13210282	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[EUR][1000 genomes]
rs13210391	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs13220866	0.81[AMR][1000 genomes]
rs2326407	0.90[EUR][1000 genomes]
rs2745454	1.00[CHD][hapmap]
rs34094324	0.90[EUR][1000 genomes]
rs34200917	0.90[EUR][1000 genomes]
rs608917	0.81[EUR][1000 genomes]
rs622859	0.81[EUR][1000 genomes]
rs627902	0.81[EUR][1000 genomes]
rs6597030	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[EUR][1000 genomes]
rs71547255	0.81[AMR][1000 genomes]
rs71553906	0.90[EUR][1000 genomes]
rs7742642	0.85[EUR][1000 genomes]
rs853421	0.81[EUR][1000 genomes]
rs853422	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs9328218	0.81[AMR][1000 genomes]
rs9328222	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[EUR][1000 genomes]
rs9689605	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[EUR][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	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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	56 gene(s)	inside rSNPs	diseases
4	nsv1030104	chr6:4062894-4240269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
5	esv2422231	chr6:4100333-4233454	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	esv2422457	chr6:4100333-4377396	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs715165	PRPF4B	cis	parietal	SCAN
rs715165	RREB1	cis	cerebellum	SCAN
rs715165	F13A1	cis	parietal	SCAN
rs715165	FOXF2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4090800-4103000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:4092600-4103000	Weak transcription	Pancreas	Pancrea
3	chr6:4098000-4101000	Weak transcription	Gastric	stomach
4	chr6:4098400-4101000	Weak transcription	HepG2	liver

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