Variant report

Variant	rs12906549
Chromosome Location	chr15:39793697-39793698
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39788869..39791943-chr15:39792558..39796121,3	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11070216	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1159994	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1159995	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11629737	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11639087	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12591824	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12592357	0.86[CHB][hapmap]
rs12594419	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13379836	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1351166	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1478606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1947783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2199657	0.99[EUR][1000 genomes]
rs2411292	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4924365	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4924366	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6492900	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap]
rs7169338	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs719964	0.86[CHB][hapmap]
rs8038823	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs8042244	0.86[ASN][1000 genomes]
rs875682	0.84[ASN][1000 genomes]
rs899285	0.88[ASN][1000 genomes]
rs936532	0.87[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	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39788000-39794000	Enhancers	NHDF-Ad	bronchial
2	chr15:39788000-39795400	Enhancers	Fetal Stomach	stomach
3	chr15:39788200-39795400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:39789000-39794400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr15:39789000-39800800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:39789000-39803200	Weak transcription	Left Ventricle	heart
7	chr15:39790200-39794400	Weak transcription	K562	blood
8	chr15:39791000-39795400	Weak transcription	Fetal Thymus	thymus
9	chr15:39791200-39794400	Weak transcription	Placenta	Placenta
10	chr15:39791400-39794400	Weak transcription	Fetal Intestine Large	intestine
11	chr15:39791600-39794400	Weak transcription	Osteobl	bone
12	chr15:39791600-39796600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:39791600-39803200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr15:39791600-39803400	Weak transcription	Fetal Lung	lung
15	chr15:39791800-39793800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr15:39791800-39794800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:39792200-39794000	Weak transcription	Colon Smooth Muscle	Colon
18	chr15:39792200-39803600	Weak transcription	Ovary	ovary
19	chr15:39792400-39796400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr15:39793000-39794600	Enhancers	Fetal Muscle Trunk	muscle
21	chr15:39793200-39794600	Enhancers	Fetal Muscle Leg	muscle
22	chr15:39793200-39795200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:39793200-39795600	Enhancers	NHEK	skin
24	chr15:39793400-39793800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:39793400-39794000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr15:39793400-39794000	Enhancers	HSMMtube	muscle
27	chr15:39793400-39794000	Enhancers	NHLF	lung
28	chr15:39793400-39794400	Enhancers	Esophagus	oesophagus
29	chr15:39793400-39794400	Enhancers	Fetal Heart	heart
30	chr15:39793400-39795400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:39793400-39795600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:39793600-39793800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:39793600-39793800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr15:39793600-39793800	Enhancers	Right Atrium	heart
35	chr15:39793600-39793800	Enhancers	Stomach Smooth Muscle	stomach
36	chr15:39793600-39794000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:39793600-39794000	Enhancers	Lung	lung
38	chr15:39793600-39794000	Enhancers	GM12878-XiMat	blood
39	chr15:39793600-39794000	Enhancers	HSMM	muscle
40	chr15:39793600-39794000	Enhancers	NH-A	brain
41	chr15:39793600-39795400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr15:39793600-39795600	Enhancers	HMEC	breast

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