Variant report

Variant	rs28858412
Chromosome Location	chr15:56739728-56739729
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10220822	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10851607	0.94[AMR][1000 genomes]
rs11071265	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12050881	0.98[ASN][1000 genomes]
rs12438639	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12443042	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12443087	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12591109	0.89[ASN][1000 genomes]
rs1402173	0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1426065	0.92[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs16976919	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2162216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2681977	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2725842	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28408704	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58619937	0.91[ASN][1000 genomes]
rs7177904	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8023554	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][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	nsv1545	chr15:56659498-56897381	Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1046891	chr15:56659587-56792033	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv471330	chr15:56659709-56896385	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv471506	chr15:56659709-56896385	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv498847	chr15:56667038-56896395	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv2525559	chr15:56669294-56897412	Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv433294	chr15:56676457-56853535	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3693203	chr15:56676457-56894478	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv35150	chr15:56677730-56896304	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv9270	chr15:56686946-56760420	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	esv2757602	chr15:56736478-56790080	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv2760033	chr15:56736478-56790080	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56716000-56756600	Weak transcription	HSMM	muscle
2	chr15:56718600-56756200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr15:56719200-56742400	Weak transcription	Fetal Intestine Large	intestine
4	chr15:56720800-56740600	Weak transcription	GM12878-XiMat	blood
5	chr15:56722800-56746800	Weak transcription	Thymus	Thymus
6	chr15:56723400-56756600	Weak transcription	Fetal Stomach	stomach
7	chr15:56732200-56756800	Weak transcription	Fetal Brain Male	brain
8	chr15:56732800-56742000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:56733000-56739800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:56734800-56751200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr15:56735000-56739800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:56735200-56740200	Weak transcription	Osteobl	bone
13	chr15:56735200-56756400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr15:56735400-56739800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:56735400-56756600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr15:56735600-56756400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:56735600-56756600	Weak transcription	Brain Anterior Caudate	brain
18	chr15:56736000-56751200	Weak transcription	Fetal Thymus	thymus
19	chr15:56736400-56755200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr15:56736800-56754400	Weak transcription	Fetal Kidney	kidney
21	chr15:56738400-56756200	Weak transcription	Fetal Lung	lung
22	chr15:56738600-56743400	Weak transcription	Dnd41	blood
23	chr15:56739600-56756600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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