Variant report

Variant	rs1549452
Chromosome Location	chr15:56702355-56702356
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MNS1-1	chr15:56701994-56702384	ENSG00000261823.1

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11630363	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11633374	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11855094	0.95[CHB][hapmap]
rs12900678	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12905782	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12908734	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1402177	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1477590	0.89[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs1554410	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16976890	0.95[CHB][hapmap]
rs17819438	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2114183	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2249090	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs2303441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2460646	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2460650	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs2554287	0.95[CHB][hapmap]
rs2682019	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2682021	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2682023	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2682051	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap]
rs2682053	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs2682054	1.00[CEU][hapmap]
rs2682059	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs2713924	1.00[CEU][hapmap]
rs2713933	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2713935	0.81[CEU][hapmap]
rs2713936	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2718901	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2718908	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2718921	0.95[CHB][hapmap]
rs2718934	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs2718941	1.00[CEU][hapmap]
rs2725854	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs2725856	0.86[CHB][hapmap]
rs2725862	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2947021	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34755898	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35497167	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35863560	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3784552	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3817406	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3985758	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4774859	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62022122	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022127	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62022133	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6493856	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493858	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7170307	0.89[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs7174892	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7181235	0.95[CHB][hapmap]
rs7181320	0.89[CEU][hapmap]
rs7496402	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs795786	0.82[CHB][hapmap]
rs795790	0.82[CEU][hapmap]
rs795791	0.91[CHB][hapmap]
rs795800	0.95[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1545	chr15:56659498-56897381	Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS 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	4 gene(s)	inside rSNPs	diseases
2	nsv1046891	chr15:56659587-56792033	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv471330	chr15:56659709-56896385	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv471506	chr15:56659709-56896385	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv904246	chr15:56665827-56732192	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv498847	chr15:56667038-56896395	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv2525559	chr15:56669294-56897412	Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv433294	chr15:56676457-56853535	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv3693203	chr15:56676457-56894478	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv35150	chr15:56677730-56896304	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv510662	chr15:56686353-56735547	Strong transcription Weak transcription ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv9270	chr15:56686946-56760420	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	esv1811649	chr15:56702355-56714618	Weak transcription Enhancers ZNF genes & repeats Strong transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1549452	FLJ12994	cis	multi-tissue	Pritchard

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56665200-56733400	Weak transcription	Fetal Kidney	kidney
2	chr15:56677600-56709600	Weak transcription	Fetal Lung	lung
3	chr15:56677800-56726200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr15:56686000-56734600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr15:56690000-56717400	Weak transcription	Dnd41	blood
6	chr15:56690000-56737800	Weak transcription	Stomach Mucosa	stomach
7	chr15:56699000-56706000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:56699200-56717800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr15:56701400-56705200	Weak transcription	Small Intestine	intestine
10	chr15:56701800-56706800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr15:56702000-56704000	Enhancers	GM12878-XiMat	blood

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