Variant report

Variant	rs28478387
Chromosome Location	chr15:93324324-93324325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RGMA-3	chr15:93322987-93324722	ENSG00000260361.1
2	lnc-CHD2-10	chr15:93322899-93324725	NONHSAT049659
3	lnc-RGMA-3	chr15:93323486-93324722	NONHSAT049661

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs13329077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28478893	1.00[AMR][1000 genomes]
rs28541685	1.00[AMR][1000 genomes]
rs28558225	1.00[AMR][1000 genomes]
rs28573371	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28699100	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28797021	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28809217	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28836190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7182474	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
2	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
3	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
4	nsv1042292	chr15:93286333-93374887	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
5	nsv984199	chr15:93288362-93381522	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription 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	55 gene(s)	inside rSNPs	diseases
6	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93304800-93344800	Weak transcription	Aorta	Aorta
2	chr15:93313000-93330400	Weak transcription	Lung	lung
3	chr15:93315000-93325200	Weak transcription	Right Ventricle	heart
4	chr15:93315400-93340200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr15:93315400-93340400	Weak transcription	Pancreas	Pancrea
6	chr15:93315400-93340600	Weak transcription	Ovary	ovary
7	chr15:93316400-93338200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr15:93322800-93324600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
9	chr15:93322800-93327200	Weak transcription	Fetal Lung	lung
10	chr15:93323200-93324400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
11	chr15:93323200-93325600	Enhancers	Fetal Brain Female	brain
12	chr15:93323200-93330600	Weak transcription	Fetal Stomach	stomach
13	chr15:93323400-93324800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr15:93323400-93340400	Weak transcription	Hela-S3	cervix
15	chr15:93323600-93325000	Enhancers	Fetal Brain Male	brain
16	chr15:93323600-93325600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:93323800-93324800	Weak transcription	Brain Germinal Matrix	brain
18	chr15:93323800-93338800	Weak transcription	Liver	Liver
19	chr15:93324000-93324400	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr15:93324000-93324600	Enhancers	Brain Angular Gyrus	brain
21	chr15:93324200-93328000	Weak transcription	Brain Hippocampus Middle	brain
22	chr15:93324200-93344600	Weak transcription	Rectal Mucosa Donor 31	rectum

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