Variant report

Variant	rs2039554
Chromosome Location	chr13:80385368-80385369
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10507900	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11619959	0.87[EUR][1000 genomes]
rs12019641	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12428029	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12867107	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1335288	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2039555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2039556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2152226	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2248413	0.85[EUR][1000 genomes]
rs2248563	0.82[EUR][1000 genomes]
rs2329137	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2329138	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2783085	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2802634	0.81[EUR][1000 genomes]
rs2802640	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2802641	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35661635	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4885658	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4885660	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4885669	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4885670	0.86[ASN][1000 genomes]
rs7322877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7327527	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7984156	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9530958	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9530959	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9545191	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9545203	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9545205	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv900588	chr13:80216846-80421340	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv900590	chr13:80342186-80421340	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr13:80377400-80385400	Weak transcription	Brain Hippocampus Middle	brain
2	chr13:80378400-80385800	Weak transcription	Primary B cells from peripheral blood	blood
3	chr13:80378400-80386000	Weak transcription	Spleen	Spleen
4	chr13:80378400-80386400	Weak transcription	Thymus	Thymus
5	chr13:80383400-80386000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr13:80383800-80386000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr13:80383800-80386200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr13:80384000-80385400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr13:80384000-80385600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:80384000-80386000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr13:80384000-80386000	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr13:80384000-80386000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr13:80384000-80386200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr13:80384000-80386600	Enhancers	Fetal Heart	heart
15	chr13:80384000-80387800	Enhancers	HUVEC	blood vessel
16	chr13:80384200-80385600	Enhancers	HMEC	breast
17	chr13:80384200-80385800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr13:80384200-80385800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr13:80384200-80386200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr13:80384200-80386200	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr13:80384400-80385600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr13:80384400-80385600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr13:80384400-80385600	Enhancers	Fetal Lung	lung
24	chr13:80384400-80385800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr13:80384400-80386000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr13:80384400-80386200	Enhancers	A549	lung
27	chr13:80384600-80385400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr13:80384600-80385400	Enhancers	Fetal Muscle Leg	muscle
29	chr13:80384600-80385600	Enhancers	Muscle Satellite Cultured Cells	--
30	chr13:80384600-80385600	Enhancers	Osteobl	bone
31	chr13:80384600-80385800	Enhancers	NHEK	skin
32	chr13:80384600-80386400	Enhancers	NHDF-Ad	bronchial
33	chr13:80384800-80385600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr13:80384800-80385600	Enhancers	Fetal Kidney	kidney
35	chr13:80384800-80385800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr13:80384800-80385800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr13:80384800-80386200	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr13:80385000-80385400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr13:80385000-80385600	Weak transcription	GM12878-XiMat	blood
40	chr13:80385000-80386000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr13:80385200-80385600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr13:80385200-80386200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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