Variant report

Variant	rs12965898
Chromosome Location	chr18:7825625-7825626
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10502362	1.00[CEU][hapmap];0.90[GIH][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11081345	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1117814	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12457653	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1348104	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs1348407	0.84[CEU][hapmap]
rs1440995	1.00[CEU][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes]
rs1440999	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs1441000	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1441001	0.92[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1443607	0.85[CEU][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap]
rs1443609	0.85[CEU][hapmap]
rs1443610	0.85[CEU][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap]
rs1443611	0.82[CEU][hapmap]
rs1443613	0.81[CEU][hapmap]
rs1443614	0.84[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap]
rs1443616	0.89[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap]
rs1530389	0.85[CEU][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap]
rs1822456	0.86[EUR][1000 genomes]
rs2009770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099790	0.85[CEU][hapmap]
rs2197010	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2377575	0.86[EUR][1000 genomes]
rs2377576	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2377577	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs331414	0.93[EUR][1000 genomes]
rs331415	0.89[CEU][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs331418	0.85[CEU][hapmap];0.87[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs331419	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs331425	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs331426	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs34294315	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs36188935	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs364418	0.81[CEU][hapmap];0.87[GIH][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs385769	0.81[GIH][hapmap]
rs4797302	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4798598	0.92[CEU][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs4798599	0.86[EUR][1000 genomes]
rs4798600	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4798601	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4798602	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4798603	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs631574	0.81[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs6506535	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs6506536	0.89[CEU][hapmap]
rs6506538	0.85[CEU][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap]
rs671369	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs694096	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs7227367	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7228457	0.87[EUR][1000 genomes]
rs7232793	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7233704	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7235300	0.96[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7239136	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs7243673	0.96[CEU][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs727949	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs727951	0.89[CEU][hapmap];0.97[GIH][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8083298	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8089088	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8095400	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8095467	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8098502	0.88[EUR][1000 genomes]
rs9944547	0.81[AMR][1000 genomes];0.86[EUR][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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv576425	chr18:7747873-7859757	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1062454	chr18:7784432-7838015	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12965898	PTPRM	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7815400-7843800	Weak transcription	A549	lung
2	chr18:7815600-7826400	Weak transcription	HepG2	liver
3	chr18:7818200-7839400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr18:7820000-7826200	Enhancers	Right Ventricle	heart
5	chr18:7821800-7836200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr18:7822400-7826200	Enhancers	Left Ventricle	heart
7	chr18:7822600-7826200	Enhancers	Fetal Muscle Leg	muscle
8	chr18:7822600-7826200	Enhancers	Right Atrium	heart
9	chr18:7822800-7825800	Enhancers	Fetal Muscle Trunk	muscle
10	chr18:7823000-7825800	Enhancers	Adipose Nuclei	Adipose
11	chr18:7823200-7825800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr18:7823200-7825800	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr18:7823400-7826600	Weak transcription	Fetal Stomach	stomach
14	chr18:7823400-7832200	Weak transcription	Fetal Lung	lung
15	chr18:7823600-7830600	Weak transcription	Fetal Heart	heart
16	chr18:7824400-7828400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr18:7824400-7828400	Weak transcription	Pancreas	Pancrea
18	chr18:7824400-7838600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr18:7825000-7827800	Weak transcription	Psoas Muscle	Psoas
20	chr18:7825000-7828400	Weak transcription	Lung	lung
21	chr18:7825000-7830200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr18:7825200-7827800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr18:7825200-7839800	Weak transcription	Thymus	Thymus
24	chr18:7825400-7827400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr18:7825400-7839600	Weak transcription	Fetal Thymus	thymus
26	chr18:7825600-7826200	Enhancers	Aorta	Aorta

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