Variant report

Variant	rs9946325
Chromosome Location	chr18:7665427-7665428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10153440	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11877002	0.91[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1446080	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1664983	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16952257	0.91[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16952260	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1940347	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1941136	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2032176	0.90[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2032177	0.82[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.82[ASN][1000 genomes]
rs28470267	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28750977	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28788217	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55750787	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506520	0.91[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6506523	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6506524	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6650627	0.91[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6650628	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7228736	0.91[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7232258	0.91[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9955885	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9956880	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9961570	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9961754	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064597	chr18:7169490-7762738	Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv543636	chr18:7169490-7762738	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv458016	chr18:7488133-7934001	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv576399	chr18:7488133-7934001	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2762810	chr18:7492090-7924728	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1062911	chr18:7561991-8088274	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv543637	chr18:7561991-8088274	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1064345	chr18:7562051-8088274	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv543638	chr18:7562051-8088274	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9946325	PTPRM	cis	cerebellum	SCAN
rs9946325	SNORD116-29	trans	lymphoblastoid	seeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7657000-7668400	Weak transcription	Gastric	stomach
2	chr18:7657400-7680600	Weak transcription	Ovary	ovary
3	chr18:7657800-7668400	Weak transcription	Spleen	Spleen
4	chr18:7657800-7669200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr18:7658000-7669200	Weak transcription	Fetal Stomach	stomach
6	chr18:7659000-7668200	Weak transcription	A549	lung
7	chr18:7659600-7668200	Weak transcription	HepG2	liver
8	chr18:7661600-7669200	Weak transcription	Aorta	Aorta
9	chr18:7663600-7666200	Weak transcription	Brain Anterior Caudate	brain
10	chr18:7663800-7668200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr18:7663800-7668400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr18:7664000-7668400	Weak transcription	Pancreas	Pancrea
13	chr18:7664200-7668200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr18:7664200-7668400	Weak transcription	Adipose Nuclei	Adipose
15	chr18:7664200-7676400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr18:7664400-7666400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr18:7664600-7668000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr18:7664600-7668200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr18:7664600-7668200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr18:7664600-7668200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr18:7664600-7668400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr18:7664600-7668400	Weak transcription	Right Atrium	heart
23	chr18:7664600-7668600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr18:7664600-7668600	Weak transcription	Lung	lung
25	chr18:7664600-7669200	Weak transcription	Fetal Muscle Leg	muscle
26	chr18:7664800-7666200	Weak transcription	Psoas Muscle	Psoas
27	chr18:7664800-7668200	Weak transcription	Left Ventricle	heart
28	chr18:7664800-7674800	Weak transcription	Fetal Heart	heart
29	chr18:7664800-7676000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr18:7665000-7666800	Weak transcription	Fetal Lung	lung
31	chr18:7665000-7668200	Weak transcription	Right Ventricle	heart
32	chr18:7665200-7667000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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