Variant report

Variant	rs12592408
Chromosome Location	chr15:34424181-34424182
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10162748	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10438390	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs10851943	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072971	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11072982	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11853022	1.00[CHB][hapmap]
rs12440568	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12595294	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236847	1.00[CHB][hapmap]
rs7167700	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7168415	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456789	chr15:34034421-34426618	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv568920	chr15:34034421-34426618	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1035579	chr15:34363159-34501115	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12592408	RP11-323I15.2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34414400-34426400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr15:34415400-34434600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:34415600-34424400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr15:34415600-34429200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:34415600-34431400	Weak transcription	NH-A	brain
6	chr15:34415600-34432800	Weak transcription	Osteobl	bone
7	chr15:34415800-34432800	Weak transcription	NHDF-Ad	bronchial
8	chr15:34416200-34439200	Weak transcription	HUVEC	blood vessel
9	chr15:34417600-34431400	Weak transcription	HSMMtube	muscle
10	chr15:34417600-34439400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr15:34417800-34436800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:34419200-34431200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr15:34419400-34429200	Weak transcription	Placenta	Placenta
14	chr15:34419400-34429800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr15:34419400-34430600	Weak transcription	HMEC	breast
16	chr15:34419400-34434800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr15:34419400-34441800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:34419600-34426200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:34421800-34425000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr15:34421800-34431600	Weak transcription	HSMM	muscle
21	chr15:34422000-34425800	Weak transcription	A549	lung
22	chr15:34422000-34429400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:34422000-34431400	Weak transcription	Primary T cells from cord blood	blood
24	chr15:34422600-34431000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr15:34423600-34430200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:34423600-34434600	Weak transcription	Left Ventricle	heart

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