Variant report

Variant	rs6506538
Chromosome Location	chr18:7855868-7855869
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10502362	0.85[CEU][hapmap]
rs12457653	0.92[CEU][hapmap]
rs12608415	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12965898	0.85[CEU][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap]
rs1348104	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs1348407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1348408	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1440995	0.85[CEU][hapmap]
rs1440999	0.85[CEU][hapmap]
rs1441000	0.85[CEU][hapmap]
rs1441001	0.85[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap]
rs1443607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443608	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443611	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443612	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443613	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443614	1.00[CEU][hapmap];0.86[GIH][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes]
rs1443616	0.88[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1530389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561654	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1596382	0.85[AMR][1000 genomes]
rs1822454	0.82[AMR][1000 genomes]
rs1838187	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1992373	0.82[AMR][1000 genomes]
rs2009770	0.85[CEU][hapmap]
rs2099790	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2377578	0.85[AMR][1000 genomes]
rs331415	0.81[CEU][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap]
rs6506535	0.88[CEU][hapmap]
rs6506536	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs671369	0.85[CEU][hapmap]
rs7235300	0.89[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap]
rs7240568	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7243673	0.81[CEU][hapmap]
rs727949	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs727951	0.88[CEU][hapmap];0.84[GIH][hapmap];0.91[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6506538	TWSG1	cis	cerebellum	SCAN
rs6506538	PTPRM	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7844800-7856600	Weak transcription	Thymus	Thymus
2	chr18:7845000-7856800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr18:7847400-7856400	Weak transcription	Left Ventricle	heart
4	chr18:7847400-7857600	Weak transcription	Lung	lung
5	chr18:7848000-7856800	Weak transcription	Right Ventricle	heart
6	chr18:7853400-7856400	Weak transcription	Right Atrium	heart
7	chr18:7854200-7856000	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr18:7854200-7857600	Enhancers	A549	lung
9	chr18:7854400-7857200	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr18:7854800-7856000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr18:7855000-7856200	Enhancers	Stomach Smooth Muscle	stomach
12	chr18:7855000-7858000	Enhancers	Hela-S3	cervix
13	chr18:7855200-7856000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr18:7855200-7856200	Enhancers	Colon Smooth Muscle	Colon
15	chr18:7855200-7857600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr18:7855200-7857600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr18:7855200-7857600	Enhancers	Psoas Muscle	Psoas
18	chr18:7855200-7857800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr18:7855400-7856400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr18:7855400-7856400	Weak transcription	Pancreas	Pancrea
21	chr18:7855400-7856400	Weak transcription	HMEC	breast
22	chr18:7855600-7856400	Flanking Active TSS	Fetal Heart	heart
23	chr18:7855600-7856600	Weak transcription	Aorta	Aorta
24	chr18:7855800-7856200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr18:7855800-7857000	Enhancers	Muscle Satellite Cultured Cells	--
26	chr18:7855800-7857000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr18:7855800-7857200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr18:7855800-7857400	Enhancers	NHEK	skin
29	chr18:7855800-7857400	Enhancers	Osteobl	bone
30	chr18:7855800-7857600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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