Variant report

Variant	rs2899377
Chromosome Location	chr15:45542643-45542644
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10450971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440127	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898733	0.98[ASN][1000 genomes]
rs1611896	0.95[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1617207	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1625404	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1625779	0.86[ASN][1000 genomes]
rs1628717	0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1632144	0.86[ASN][1000 genomes]
rs1648280	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1648284	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1648288	0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1648290	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1648291	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1648292	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1648296	0.98[ASN][1000 genomes]
rs1648297	0.88[ASN][1000 genomes]
rs1648298	0.84[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1648299	0.94[ASN][1000 genomes]
rs1648300	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1648301	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1648314	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1648315	0.85[ASN][1000 genomes]
rs1706765	0.94[JPT][hapmap]
rs1706779	1.00[JPT][hapmap]
rs1706819	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1706823	0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1706828	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1706833	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1706836	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292468	0.83[JPT][hapmap]
rs2413777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458238	0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2458240	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2458241	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2467839	0.85[ASN][1000 genomes]
rs2668738	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2668750	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2899376	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58701250	0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7167481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732622	0.91[ASN][1000 genomes]
rs938129	1.00[JPT][hapmap]
rs938130	0.81[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45537200-45547400	Weak transcription	Gastric	stomach
2	chr15:45539400-45547000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr15:45541400-45544000	Weak transcription	Stomach Mucosa	stomach
4	chr15:45541400-45544800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr15:45541800-45544400	Weak transcription	Brain Angular Gyrus	brain
6	chr15:45541800-45545000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr15:45542000-45544000	Weak transcription	Fetal Intestine Small	intestine
8	chr15:45542000-45544400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr15:45542000-45547000	Weak transcription	HepG2	liver
10	chr15:45542000-45547200	Weak transcription	Aorta	Aorta
11	chr15:45542400-45549600	Weak transcription	Left Ventricle	heart

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