Variant report

Variant	rs385769
Chromosome Location	chr18:7800480-7800481
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12965898	0.81[GIH][hapmap]
rs1441001	0.81[GIH][hapmap]
rs1443616	0.81[GIH][hapmap]
rs331415	0.85[MEX][hapmap]
rs331418	0.89[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs331419	0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs331425	0.85[CEU][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs331426	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs364418	0.82[CEU][hapmap];0.89[GIH][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs620216	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs631574	0.86[ASW][hapmap];0.82[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs638251	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs653973	0.80[MEX][hapmap]
rs655078	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs694096	0.83[EUR][1000 genomes]
rs7235300	0.81[GIH][hapmap]
rs789451	1.00[JPT][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs385769	PTPRM	cis	cerebellum	SCAN
rs385769	TWSG1	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7766800-7811200	Weak transcription	Aorta	Aorta
2	chr18:7767200-7812400	Weak transcription	Pancreas	Pancrea
3	chr18:7787600-7804200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr18:7787800-7806600	Weak transcription	Thymus	Thymus
5	chr18:7789800-7804000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr18:7790400-7802000	Weak transcription	HepG2	liver
7	chr18:7790600-7813400	Weak transcription	Fetal Thymus	thymus
8	chr18:7791200-7807800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr18:7794400-7806000	Weak transcription	Lung	lung
10	chr18:7794400-7809000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr18:7795400-7806600	Weak transcription	Psoas Muscle	Psoas
12	chr18:7796000-7811600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr18:7797200-7804200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr18:7797600-7806000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr18:7797800-7802000	Weak transcription	Left Ventricle	heart
16	chr18:7797800-7804000	Weak transcription	Right Atrium	heart
17	chr18:7798000-7809200	Weak transcription	Right Ventricle	heart
18	chr18:7798200-7803800	Weak transcription	A549	lung
19	chr18:7799400-7800600	Weak transcription	Ovary	ovary
20	chr18:7800000-7800600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr18:7800200-7801000	Enhancers	Fetal Heart	heart
22	chr18:7800200-7812200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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