Variant report

Variant	rs345759
Chromosome Location	chr15:33407543-33407544
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1454987	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1902148	0.86[ASN][1000 genomes]
rs2085180	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2085181	0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2257131	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2444953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2444956	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2444960	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2444962	0.86[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2444964	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2444965	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2444966	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2444967	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2444969	0.82[ASN][1000 genomes]
rs2444970	0.84[ASN][1000 genomes]
rs2444972	0.82[ASN][1000 genomes]
rs2444973	0.82[ASN][1000 genomes]
rs2444974	0.82[ASN][1000 genomes]
rs2444975	0.82[ASN][1000 genomes]
rs2468741	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2468746	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2468748	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2468749	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2468750	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2468752	0.84[ASN][1000 genomes]
rs2468755	0.82[ASN][1000 genomes]
rs345762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3861197	0.86[ASN][1000 genomes]
rs4780082	0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.88[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs345759	TRPM1	cis	cerebellum	SCAN
rs345759	SCG5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33403600-33407600	Weak transcription	Fetal Heart	heart
2	chr15:33403600-33411400	Weak transcription	HSMM	muscle
3	chr15:33403800-33411400	Weak transcription	HSMMtube	muscle
4	chr15:33404000-33407600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:33404000-33407800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:33404000-33407800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr15:33404000-33407800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr15:33404000-33407800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:33404000-33408400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr15:33404800-33408000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:33405200-33407600	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr15:33405200-33407800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr15:33405200-33408000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr15:33405200-33409400	Weak transcription	Fetal Kidney	kidney
15	chr15:33405400-33407800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr15:33405800-33407800	Enhancers	Fetal Lung	lung
17	chr15:33406200-33408000	Enhancers	Fetal Thymus	thymus
18	chr15:33406400-33408000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr15:33406400-33408000	Enhancers	Placenta	Placenta
20	chr15:33406400-33408000	Enhancers	NHLF	lung
21	chr15:33406400-33410200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:33406400-33411400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:33406400-33411400	Weak transcription	Pancreas	Pancrea
24	chr15:33406400-33418200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr15:33406800-33418400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:33407000-33408200	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr15:33407000-33409600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr15:33407000-33418400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:33407200-33407600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:33407400-33408000	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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