Variant report

Variant	rs28409161
Chromosome Location	chr15:33250654-33250655
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	chr15:33244592..33247228-chr15:33248722..33251718,2	MCF-7	breast:
2	chr15:33244808..33246374-chr15:33249318..33251534,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12900473	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12914123	0.80[EUR][1000 genomes]
rs28393295	0.83[EUR][1000 genomes]
rs28439064	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28456225	0.80[EUR][1000 genomes]
rs28463080	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28475199	0.80[EUR][1000 genomes]
rs28475311	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28485200	0.80[EUR][1000 genomes]
rs28544912	0.80[EUR][1000 genomes]
rs28562592	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28591666	0.80[EUR][1000 genomes]
rs28661574	0.80[EUR][1000 genomes]
rs34953485	0.80[EUR][1000 genomes]
rs35147427	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67543125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162402	0.80[EUR][1000 genomes]
rs8029078	0.80[EUR][1000 genomes]
rs8032279	0.80[EUR][1000 genomes]
rs8033449	0.80[EUR][1000 genomes]
rs8033969	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456785	chr15:32926076-33352989	Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv568913	chr15:32926076-33352989	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv903978	chr15:33144202-33308641	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	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
5	nsv1041609	chr15:33148035-33355999	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv542339	chr15:33148035-33355999	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv903980	chr15:33149087-33264201	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	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
9	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
10	nsv568917	chr15:33167171-33304172	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	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
12	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28409161	RBPMS2	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33232800-33263400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:33238200-33259600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr15:33243800-33258800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr15:33243800-33264400	Weak transcription	Gastric	stomach
5	chr15:33244200-33253800	Weak transcription	Lung	lung
6	chr15:33245200-33274800	Weak transcription	Thymus	Thymus
7	chr15:33245600-33259800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr15:33246000-33251200	Weak transcription	Fetal Muscle Leg	muscle
9	chr15:33246000-33251600	Weak transcription	Stomach Mucosa	stomach
10	chr15:33247600-33253800	Weak transcription	Fetal Kidney	kidney
11	chr15:33247800-33251600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:33248600-33254200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr15:33248800-33251400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr15:33249000-33251200	Weak transcription	HSMM	muscle
15	chr15:33249000-33252600	Weak transcription	Aorta	Aorta
16	chr15:33249200-33250800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:33249200-33250800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:33249200-33251400	Weak transcription	NHDF-Ad	bronchial
19	chr15:33249200-33251600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:33249200-33259200	Weak transcription	HSMMtube	muscle
21	chr15:33249200-33262800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr15:33249200-33277800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr15:33249400-33251000	Weak transcription	NHLF	lung
24	chr15:33249400-33251200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:33249400-33251200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:33249400-33251400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr15:33249400-33263000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr15:33249800-33250800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:33250000-33251400	Weak transcription	Osteobl	bone
30	chr15:33250600-33251400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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