Variant report

Variant	rs558290
Chromosome Location	chr15:55927698-55927699
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11638787	0.91[ASN][1000 genomes]
rs12591646	0.90[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs1659296	0.84[AFR][1000 genomes]
rs16976428	0.91[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs16976436	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs28398229	0.92[ASN][1000 genomes]
rs28512199	0.89[ASN][1000 genomes]
rs3910565	0.89[ASN][1000 genomes]
rs4601983	0.82[ASN][1000 genomes]
rs4774796	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[ASN][1000 genomes]
rs489672	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs491014	0.87[ASW][hapmap];0.94[YRI][hapmap]
rs530798	0.87[ASW][hapmap];0.81[LWK][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes]
rs581287	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59647323	0.87[ASN][1000 genomes]
rs654844	0.85[AFR][1000 genomes]
rs7163167	0.86[MEX][hapmap]
rs7164393	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs720509	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8025445	0.81[CEU][hapmap]
rs8027131	0.84[AFR][1000 genomes]
rs9920740	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1040917	chr15:55562940-55943942	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv1041635	chr15:55658171-55943942	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1049774	chr15:55759573-56044600	Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv569540	chr15:55866065-55950082	Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55902200-55942200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:55904600-55929400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:55908600-55945000	Weak transcription	Left Ventricle	heart
4	chr15:55908800-55938800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:55910200-55928600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr15:55910400-55930800	Weak transcription	Fetal Lung	lung
7	chr15:55911000-55931000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr15:55911800-55977000	Weak transcription	Fetal Intestine Small	intestine
9	chr15:55912200-55929800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:55912400-55944000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr15:55916000-55938200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:55916200-55928200	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr15:55918600-55929800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:55918600-55931200	Weak transcription	Ovary	ovary
15	chr15:55920400-55930200	Weak transcription	Placenta	Placenta
16	chr15:55920600-55930200	Weak transcription	Fetal Intestine Large	intestine
17	chr15:55920600-55931600	Weak transcription	Lung	lung
18	chr15:55920600-55933600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:55920600-55940000	Weak transcription	Psoas Muscle	Psoas
20	chr15:55920600-55953400	Weak transcription	HUVEC	blood vessel
21	chr15:55920800-55935200	Weak transcription	HSMMtube	muscle
22	chr15:55920800-55944600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr15:55920800-55987600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:55921000-55936200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:55921200-55928600	Weak transcription	Fetal Muscle Leg	muscle
26	chr15:55921200-55929200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr15:55921200-55941400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:55923400-55930800	Weak transcription	A549	lung
29	chr15:55924000-55930400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr15:55924000-55931800	Weak transcription	Brain Substantia Nigra	brain
31	chr15:55924200-55930600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:55924400-55929600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:55924400-55944800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:55924600-55928800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr15:55924600-55934600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr15:55924800-55934600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr15:55925200-55928600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:55926200-55929600	Strong transcription	Fetal Stomach	stomach
39	chr15:55927000-55928800	Strong transcription	HepG2	liver
40	chr15:55927000-55929600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr15:55927000-55929600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr15:55927400-55928400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr15:55927600-55928800	Strong transcription	Fetal Kidney	kidney
44	chr15:55927600-55931800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr15:55927600-55932800	Strong transcription	Hela-S3	cervix

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