Variant report

Variant	rs28562592
Chromosome Location	chr15:33256544-33256545
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10519766	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11852876	0.83[EUR][1000 genomes]
rs11855526	0.83[EUR][1000 genomes]
rs12900473	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12914123	0.84[EUR][1000 genomes]
rs16960803	0.81[EUR][1000 genomes]
rs16960807	0.81[EUR][1000 genomes]
rs16961611	0.83[EUR][1000 genomes]
rs2034479	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs28393295	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs28409161	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28439064	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28453761	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs28456225	0.84[EUR][1000 genomes]
rs28463080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28475199	0.84[EUR][1000 genomes]
rs28475311	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28485200	0.84[EUR][1000 genomes]
rs28508587	0.81[EUR][1000 genomes]
rs28544912	0.84[EUR][1000 genomes]
rs28591666	0.84[EUR][1000 genomes]
rs28661574	0.84[EUR][1000 genomes]
rs28719161	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs28735093	0.83[EUR][1000 genomes]
rs34953485	0.84[EUR][1000 genomes]
rs35147427	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3812936	0.83[EUR][1000 genomes]
rs41473744	0.83[EUR][1000 genomes]
rs67543125	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7162402	0.84[EUR][1000 genomes]
rs8025966	0.81[EUR][1000 genomes]
rs8029078	0.84[EUR][1000 genomes]
rs8032279	0.84[EUR][1000 genomes]
rs8033449	0.84[EUR][1000 genomes]
rs8033969	0.84[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
rs28562592	RBPMS2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 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	chr15:33245200-33274800	Weak transcription	Thymus	Thymus
6	chr15:33245600-33259800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr15:33249200-33259200	Weak transcription	HSMMtube	muscle
8	chr15:33249200-33262800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:33249200-33277800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr15:33249400-33263000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr15:33250800-33263200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:33251400-33262400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:33251600-33263000	Weak transcription	Colonic Mucosa	Colon
14	chr15:33251600-33272000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:33252000-33263600	Weak transcription	Stomach Mucosa	stomach
16	chr15:33252400-33270200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:33252400-33270800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:33254000-33258000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:33254000-33261800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr15:33254000-33267200	Weak transcription	NHLF	lung
21	chr15:33254200-33258000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr15:33254200-33258000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:33254200-33258200	Weak transcription	Lung	lung
24	chr15:33254200-33260000	Weak transcription	Fetal Kidney	kidney
25	chr15:33254800-33260200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr15:33255600-33262000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:33255800-33256600	Strong transcription	Placenta	Placenta
28	chr15:33256000-33256600	Strong transcription	HSMM	muscle
29	chr15:33256000-33258000	Weak transcription	Fetal Thymus	thymus

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