Variant report

Variant	rs1087837
Chromosome Location	chr15:56733639-56733640
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11631618	0.83[ASN][1000 genomes]
rs11632091	0.83[CEU][hapmap]
rs11638060	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11638076	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11638872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11638965	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11639320	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1711483	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs1715919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2249183	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes]
rs3848113	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55759746	0.82[EUR][1000 genomes]
rs705450	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7163544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72740562	0.81[EUR][1000 genomes]
rs72740574	0.82[EUR][1000 genomes]
rs72740578	0.82[EUR][1000 genomes]
rs72740579	0.82[EUR][1000 genomes]
rs72740592	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72742607	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72742619	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72742631	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72742636	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72742652	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72742667	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72742674	0.82[EUR][1000 genomes]
rs72742676	0.82[EUR][1000 genomes]
rs795781	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs795785	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs795793	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs813267	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1087837	MNS1	cis	brain	BrainEAC
rs1087837	MNS1	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56686000-56734600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr15:56690000-56737800	Weak transcription	Stomach Mucosa	stomach
3	chr15:56704000-56734600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:56705400-56734800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr15:56716000-56756600	Weak transcription	HSMM	muscle
6	chr15:56716800-56734600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr15:56718000-56734600	Weak transcription	Brain Anterior Caudate	brain
8	chr15:56718400-56734600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr15:56718600-56734600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr15:56718600-56734600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr15:56718600-56734600	Weak transcription	Adipose Nuclei	Adipose
12	chr15:56718600-56734800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr15:56718600-56736600	Weak transcription	Brain Hippocampus Middle	brain
14	chr15:56718600-56756200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr15:56719200-56742400	Weak transcription	Fetal Intestine Large	intestine
16	chr15:56719400-56734600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr15:56719400-56736800	Weak transcription	Fetal Muscle Leg	muscle
18	chr15:56720800-56740600	Weak transcription	GM12878-XiMat	blood
19	chr15:56721400-56737600	Weak transcription	Pancreas	Pancrea
20	chr15:56721800-56736600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr15:56722400-56736800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:56722800-56746800	Weak transcription	Thymus	Thymus
23	chr15:56723400-56734400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:56723400-56756600	Weak transcription	Fetal Stomach	stomach
25	chr15:56723600-56737400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:56723800-56734400	Weak transcription	Fetal Lung	lung
27	chr15:56725600-56734600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr15:56726400-56734600	Weak transcription	Ovary	ovary
29	chr15:56726600-56734400	Weak transcription	Fetal Thymus	thymus
30	chr15:56726600-56734600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:56731000-56738600	Strong transcription	Dnd41	blood
32	chr15:56732200-56756800	Weak transcription	Fetal Brain Male	brain
33	chr15:56732800-56742000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr15:56733000-56734600	Weak transcription	Osteobl	bone
35	chr15:56733000-56739800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr15:56733400-56735800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr15:56733400-56735800	Strong transcription	Fetal Kidney	kidney

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