Variant report

Variant	rs1454987
Chromosome Location	chr15:33420146-33420147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:33359725..33362566-chr15:33418039..33421001,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248905	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1902148	0.91[ASN][1000 genomes]
rs2085180	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2085181	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2257131	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2444953	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2444956	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2444960	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2444962	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2444964	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2444965	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2444966	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2444967	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2444969	0.86[ASN][1000 genomes]
rs2444970	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2444972	0.86[ASN][1000 genomes]
rs2444973	0.86[ASN][1000 genomes]
rs2444974	0.86[ASN][1000 genomes]
rs2444975	0.86[ASN][1000 genomes]
rs2444976	0.84[ASN][1000 genomes]
rs2444979	0.82[ASN][1000 genomes]
rs2468741	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2468746	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2468748	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2468749	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2468750	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2468751	0.81[ASN][1000 genomes]
rs2468752	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2468755	0.86[ASN][1000 genomes]
rs2468756	0.83[ASN][1000 genomes]
rs345759	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs345762	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3861197	0.89[ASN][1000 genomes]
rs4780082	0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.89[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1454987	TRPM1	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33411800-33420200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr15:33416600-33420400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:33417400-33420200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr15:33418000-33420200	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr15:33418200-33420200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr15:33418200-33420600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:33418600-33420200	Enhancers	Hela-S3	cervix
8	chr15:33418800-33421000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:33419000-33422000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:33419000-33423800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:33419000-33423800	Weak transcription	Brain Angular Gyrus	brain
12	chr15:33419200-33420200	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr15:33419200-33420200	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr15:33419200-33420200	Enhancers	Thymus	Thymus
15	chr15:33419200-33420600	Enhancers	Fetal Thymus	thymus
16	chr15:33419200-33424200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr15:33419200-33427600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr15:33419200-33427600	Weak transcription	Lung	lung
19	chr15:33419200-33428600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr15:33419200-33430000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr15:33419200-33430400	Weak transcription	Psoas Muscle	Psoas
22	chr15:33419400-33420200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:33419400-33420200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:33419400-33420200	Enhancers	HSMM	muscle
25	chr15:33419400-33420400	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr15:33419400-33420400	Enhancers	NHDF-Ad	bronchial
27	chr15:33419400-33423600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr15:33419400-33423600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr15:33419400-33423800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr15:33419600-33420200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:33419600-33420400	Enhancers	NHLF	lung
32	chr15:33419600-33423600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr15:33419600-33423600	Weak transcription	Fetal Lung	lung
34	chr15:33419600-33423600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr15:33419600-33423600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:33419600-33423600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr15:33419600-33423600	Weak transcription	NHEK	skin
38	chr15:33419600-33423800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:33419600-33423800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr15:33419600-33423800	Weak transcription	HSMMtube	muscle
41	chr15:33419600-33423800	Weak transcription	HUVEC	blood vessel
42	chr15:33419600-33423800	Weak transcription	NH-A	brain
43	chr15:33419600-33424000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr15:33419600-33424000	Weak transcription	Primary T cells from cord blood	blood
45	chr15:33419600-33424000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr15:33419800-33420200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr15:33419800-33423800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr15:33419800-33423800	Weak transcription	HMEC	breast
49	chr15:33420000-33420400	Enhancers	Fetal Kidney	kidney
50	chr15:33420000-33423600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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