Variant report

Variant	rs9920539
Chromosome Location	chr15:39759179-39759180
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11070204	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1158918	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11633970	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11857561	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12438465	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12593294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12899217	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1812583	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1947782	0.85[ASN][1000 genomes]
rs1993892	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1993893	0.96[ASN][1000 genomes]
rs2086166	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2127029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2411293	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34329697	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4244571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4486853	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4924361	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4924363	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59431794	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60697424	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6492888	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7171244	0.93[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7178351	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7180041	1.00[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7350779	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74008200	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74010438	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8030260	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8032900	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs8033214	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9888722	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[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:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39740000-39759400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:39753600-39765200	Weak transcription	Pancreas	Pancrea
3	chr15:39754600-39759200	Weak transcription	Spleen	Spleen
4	chr15:39754600-39764600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr15:39754800-39763400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr15:39755800-39759400	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr15:39756000-39759800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr15:39756000-39760200	Weak transcription	HUVEC	blood vessel
9	chr15:39757400-39760000	Enhancers	NHDF-Ad	bronchial
10	chr15:39757400-39761200	Enhancers	Fetal Stomach	stomach
11	chr15:39757600-39760200	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr15:39757600-39761200	Enhancers	Fetal Muscle Leg	muscle
13	chr15:39757800-39759400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:39757800-39759600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:39758000-39759400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:39758000-39759400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:39758000-39759400	Enhancers	K562	blood
18	chr15:39758000-39759800	Enhancers	Fetal Lung	lung
19	chr15:39758000-39759800	Enhancers	Fetal Muscle Trunk	muscle
20	chr15:39758000-39759800	Enhancers	Placenta	Placenta
21	chr15:39758000-39759800	Enhancers	Left Ventricle	heart
22	chr15:39758000-39760000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:39758000-39760000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:39758000-39760000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr15:39758000-39762200	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr15:39758200-39759200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr15:39758200-39759400	Weak transcription	Right Ventricle	heart
28	chr15:39758200-39759400	Weak transcription	Stomach Mucosa	stomach
29	chr15:39758200-39759800	Enhancers	NHLF	lung
30	chr15:39758200-39765200	Weak transcription	Right Atrium	heart
31	chr15:39758400-39759400	Weak transcription	Adipose Nuclei	Adipose
32	chr15:39758400-39759400	Weak transcription	Lung	lung
33	chr15:39758400-39759800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:39758600-39759400	Weak transcription	Colon Smooth Muscle	Colon
35	chr15:39758600-39760800	Weak transcription	Osteobl	bone
36	chr15:39758800-39764000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:39758800-39765200	Weak transcription	HSMM	muscle
38	chr15:39759000-39759400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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