Variant report

Variant	rs3858866
Chromosome Location	chr13:40073609-40073610
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1475175	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1475176	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17807293	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1927196	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2018	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943668	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943669	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943670	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943671	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55838454	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6563712	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563713	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563714	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139794	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7317187	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7321906	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7322026	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7324077	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7335002	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7335427	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7335605	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7981363	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7982627	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002574	1.00[ASN][1000 genomes]
rs8002691	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912043	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs912044	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9315691	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9315692	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548785	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576824	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9594334	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9594335	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9594336	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603549	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603550	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603551	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603552	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603554	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers 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
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	esv2757529	chr13:40040036-40090742	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv2759933	chr13:40040036-40090742	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40061600-40081000	Weak transcription	Osteobl	bone
2	chr13:40064800-40081200	Weak transcription	HSMMtube	muscle
3	chr13:40065600-40075000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr13:40065600-40075200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr13:40067200-40074000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr13:40067600-40074000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr13:40067600-40074200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr13:40067800-40078400	Enhancers	Fetal Heart	heart
9	chr13:40068400-40080800	Weak transcription	Fetal Brain Female	brain
10	chr13:40069200-40075000	Weak transcription	Lung	lung
11	chr13:40069200-40080400	Weak transcription	Aorta	Aorta
12	chr13:40070200-40073800	Enhancers	H1 Cell Line	embryonic stem cell
13	chr13:40071000-40073800	Weak transcription	Adipose Nuclei	Adipose
14	chr13:40071400-40075800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr13:40071400-40077200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr13:40071800-40075600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr13:40071800-40076200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr13:40072200-40074000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr13:40072600-40075800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr13:40072800-40073800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr13:40072800-40073800	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr13:40072800-40074000	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr13:40072800-40074200	Enhancers	Ovary	ovary
24	chr13:40073000-40073800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr13:40073000-40074000	Enhancers	Right Ventricle	heart
26	chr13:40073000-40075800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr13:40073000-40076000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr13:40073000-40076000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr13:40073000-40076400	Enhancers	Psoas Muscle	Psoas
30	chr13:40073000-40076400	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr13:40073000-40076600	Enhancers	Fetal Muscle Leg	muscle
32	chr13:40073000-40077400	Enhancers	Right Atrium	heart
33	chr13:40073000-40077600	Enhancers	Left Ventricle	heart
34	chr13:40073000-40081200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr13:40073200-40075000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr13:40073200-40075800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr13:40073400-40073800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr13:40073400-40074000	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr13:40073400-40074200	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr13:40073600-40073800	Enhancers	Fetal Muscle Trunk	muscle
41	chr13:40073600-40074000	Enhancers	Brain Substantia Nigra	brain
42	chr13:40073600-40074000	Enhancers	Colon Smooth Muscle	Colon
43	chr13:40073600-40074000	Enhancers	Spleen	Spleen
44	chr13:40073600-40074200	Enhancers	Rectal Smooth Muscle	rectum
45	chr13:40073600-40074400	Enhancers	Brain Cingulate Gyrus	brain
46	chr13:40073600-40074400	Enhancers	Fetal Brain Male	brain

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