Variant report

Variant	rs1399078
Chromosome Location	chr15:33446947-33446948
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1399077	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17235784	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17235791	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs713277	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs7162655	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7165262	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723411	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026162	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027575	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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
rs1399078	TRPM1	cis	cerebellum	SCAN
rs1399078	KLF13	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33438600-33449800	Weak transcription	NHEK	skin
2	chr15:33439000-33447200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:33441000-33447000	Weak transcription	Fetal Thymus	thymus
4	chr15:33441200-33451800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:33442200-33447600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:33442200-33447600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr15:33442600-33448000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr15:33442800-33447400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr15:33443800-33447000	Weak transcription	Fetal Kidney	kidney
10	chr15:33443800-33450200	Weak transcription	Fetal Intestine Large	intestine
11	chr15:33444600-33447800	Enhancers	HMEC	breast
12	chr15:33445000-33447000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:33445000-33447200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:33445200-33447000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:33445200-33447400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:33445600-33447400	Weak transcription	Brain Angular Gyrus	brain
17	chr15:33445600-33453400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr15:33446000-33447000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr15:33446000-33449600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr15:33446200-33447000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
21	chr15:33446200-33447000	Flanking Active TSS	HSMM	muscle
22	chr15:33446200-33447400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:33446200-33448200	Enhancers	Brain Hippocampus Middle	brain
24	chr15:33446400-33447000	Enhancers	Primary hematopoietic stem cells	blood
25	chr15:33446400-33447000	Active TSS	Adipose Nuclei	Adipose
26	chr15:33446400-33447400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:33446400-33447600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr15:33446400-33448800	Enhancers	Placenta	Placenta
29	chr15:33446600-33447000	Flanking Active TSS	HSMMtube	muscle
30	chr15:33446600-33447000	Flanking Active TSS	Osteobl	bone
31	chr15:33446600-33447600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:33446600-33447600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:33446600-33447800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:33446600-33447800	Enhancers	NHDF-Ad	bronchial
35	chr15:33446800-33447400	Enhancers	Brain Cingulate Gyrus	brain
36	chr15:33446800-33447400	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr15:33446800-33447600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:33446800-33447600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:33446800-33447600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:33446800-33447600	Flanking Active TSS	Brain Substantia Nigra	brain
41	chr15:33446800-33447600	Enhancers	NH-A	brain
42	chr15:33446800-33449800	Weak transcription	Lung	lung
43	chr15:33446800-33450200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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