Variant report

Variant	rs2619172
Chromosome Location	chr15:33388684-33388685
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12440029	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12905054	0.92[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2306277	0.92[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28437311	0.88[EUR][1000 genomes]
rs345791	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs345795	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv903981	chr15:33207082-33550256	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv568918	chr15:33244672-33446971	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv903982	chr15:33282844-33616150	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv903983	chr15:33388030-33550256	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2619172	TRPM1	cis	cerebellum	SCAN
rs2619172	FMN1	cis	Esophagus Mucosa	GTEx
rs2619172	OCA2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33383000-33389800	Weak transcription	Hela-S3	cervix
2	chr15:33383000-33390000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr15:33383200-33390400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:33384800-33389600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr15:33384800-33390000	Weak transcription	HUVEC	blood vessel
6	chr15:33384800-33390400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr15:33384800-33391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:33384800-33395000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr15:33384800-33395400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr15:33385000-33389800	Weak transcription	NHEK	skin
11	chr15:33385000-33396400	Weak transcription	Fetal Kidney	kidney
12	chr15:33385200-33390200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:33385600-33389800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:33386400-33390600	Weak transcription	Fetal Muscle Leg	muscle
15	chr15:33386600-33388800	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr15:33386800-33389800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:33386800-33390400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:33387000-33389600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:33387000-33389600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr15:33387200-33388800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:33387200-33388800	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr15:33387200-33389400	Weak transcription	NHDF-Ad	bronchial
23	chr15:33387200-33389800	Weak transcription	HSMM	muscle
24	chr15:33387200-33390200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:33387200-33390400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr15:33387400-33388800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:33387400-33389600	Weak transcription	NH-A	brain
28	chr15:33388400-33389000	Enhancers	HSMMtube	muscle
29	chr15:33388400-33389200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:33388400-33389800	Weak transcription	NHLF	lung
31	chr15:33388600-33388800	Enhancers	Osteobl	bone
32	chr15:33388600-33390200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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