Variant report

Variant	rs28564029
Chromosome Location	chr15:33022208-33022209
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:33021505-33039552	IMR90	lung:	n/a	n/a
2	POLR2A	chr15:33021602-33024666	ProgFib	skin:	n/a	n/a
3	GATA3	chr15:33022064-33022464	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
GREM1	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1129456	0.80[EUR][1000 genomes]
rs17228641	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17525764	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28433691	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28436730	0.97[EUR][1000 genomes]
rs28439346	0.87[EUR][1000 genomes]
rs28473724	0.96[EUR][1000 genomes]
rs28482374	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28569405	0.84[EUR][1000 genomes]
rs28574716	0.85[EUR][1000 genomes]
rs28585618	0.89[EUR][1000 genomes]
rs28615915	0.91[EUR][1000 genomes]
rs28616589	0.85[EUR][1000 genomes]
rs28617440	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28767884	0.97[EUR][1000 genomes]
rs28768389	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28840420	0.99[EUR][1000 genomes]
rs28855511	0.84[EUR][1000 genomes]
rs3207357	0.96[EUR][1000 genomes]
rs7175986	0.97[EUR][1000 genomes]
rs8041794	0.84[EUR][1000 genomes]
rs9920024	0.91[EUR][1000 genomes]
rs9920792	0.88[AMR][1000 genomes];0.91[EUR][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	esv2422296	chr15:32798938-33221215	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv482680	chr15:32958401-33154005	Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv456787	chr15:32968923-33023951	Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv568916	chr15:32968923-33023951	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv832961	chr15:33021177-33134988	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33012000-33023200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:33012400-33023200	Weak transcription	HSMM	muscle
3	chr15:33013400-33022800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr15:33013600-33023400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr15:33017000-33024200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr15:33020400-33022600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:33020400-33023400	Weak transcription	HSMMtube	muscle
8	chr15:33021000-33023200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:33021600-33022400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr15:33021600-33023400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr15:33021800-33023400	Genic enhancers	NH-A	brain
12	chr15:33021800-33025000	Weak transcription	Brain Hippocampus Middle	brain
13	chr15:33021800-33025600	Genic enhancers	NHDF-Ad	bronchial
14	chr15:33022000-33022400	Bivalent Enhancer	Fetal Kidney	kidney
15	chr15:33022000-33023200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr15:33022000-33023200	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr15:33022000-33023200	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr15:33022000-33023200	Strong transcription	Stomach Smooth Muscle	stomach
19	chr15:33022000-33023400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:33022000-33023600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:33022000-33023600	Enhancers	NHEK	skin
22	chr15:33022000-33025200	Genic enhancers	Muscle Satellite Cultured Cells	--
23	chr15:33022000-33025200	Genic enhancers	Osteobl	bone
24	chr15:33022200-33022600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:33022200-33023200	Enhancers	H1 Cell Line	embryonic stem cell
26	chr15:33022200-33023200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
27	chr15:33022200-33023200	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr15:33022200-33024200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:33022200-33024200	Genic enhancers	NHLF	lung

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