Variant report

Variant	rs6033058
Chromosome Location	chr20:11197256-11197257
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-JAG1-10	chr20:11195308-11197530	ucscGeneNc_uc002wnx_2

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1013497	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1013498	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1016241	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327345	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3946078	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4300903	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4813964	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6033054	0.97[ASN][1000 genomes]
rs6033061	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6040427	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6078102	1.00[CHB][hapmap]
rs6104722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6108860	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs975481	0.82[EUR][1000 genomes];0.98[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	nsv1065969	chr20:10850562-11464172	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv544181	chr20:10850562-11464172	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv585415	chr20:11134907-11383327	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1056067	chr20:11174581-11213919	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:11186800-11197600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr20:11190000-11198200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr20:11195000-11198200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr20:11195000-11199800	Enhancers	Fetal Lung	lung
5	chr20:11195200-11201800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr20:11195400-11197600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr20:11195600-11197600	Weak transcription	Left Ventricle	heart
8	chr20:11195600-11197600	Weak transcription	Right Atrium	heart
9	chr20:11195600-11199000	Weak transcription	Gastric	stomach
10	chr20:11195600-11210200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr20:11195800-11197600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr20:11196000-11197400	Weak transcription	Fetal Kidney	kidney
13	chr20:11196200-11197600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr20:11196600-11197400	Enhancers	Fetal Heart	heart
15	chr20:11196600-11199400	Enhancers	Muscle Satellite Cultured Cells	--
16	chr20:11196600-11199400	Enhancers	HUVEC	blood vessel
17	chr20:11196800-11198400	Flanking Active TSS	A549	lung
18	chr20:11196800-11198400	Bivalent Enhancer	HepG2	liver
19	chr20:11196800-11199800	Enhancers	Fetal Intestine Large	intestine
20	chr20:11197000-11197600	Weak transcription	Lung	lung
21	chr20:11197000-11198200	Enhancers	NHLF	lung
22	chr20:11197000-11198600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr20:11197000-11198600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr20:11197000-11198800	Enhancers	HSMMtube	muscle
25	chr20:11197000-11199200	Enhancers	Fetal Stomach	stomach
26	chr20:11197000-11199200	Enhancers	HSMM	muscle
27	chr20:11197000-11200200	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr20:11197200-11197400	Flanking Active TSS	Osteobl	bone
29	chr20:11197200-11197800	Enhancers	Hela-S3	cervix
30	chr20:11197200-11198000	Enhancers	Adipose Nuclei	Adipose
31	chr20:11197200-11198000	Enhancers	Pancreas	Pancrea
32	chr20:11197200-11198000	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr20:11197200-11198200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr20:11197200-11198400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr20:11197200-11198400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr20:11197200-11198400	Enhancers	Aorta	Aorta
37	chr20:11197200-11198400	Enhancers	Colon Smooth Muscle	Colon
38	chr20:11197200-11198400	Enhancers	Ovary	ovary
39	chr20:11197200-11198400	Enhancers	Psoas Muscle	Psoas
40	chr20:11197200-11198400	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr20:11197200-11198600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr20:11197200-11198600	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr20:11197200-11198600	Enhancers	GM12878-XiMat	blood
44	chr20:11197200-11198600	Enhancers	NH-A	brain
45	chr20:11197200-11198600	Enhancers	NHDF-Ad	bronchial
46	chr20:11197200-11199600	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr20:11197200-11199800	Enhancers	Primary hematopoietic stem cells	blood
48	chr20:11197200-11199800	Enhancers	Fetal Muscle Leg	muscle
49	chr20:11197200-11200000	Enhancers	Fetal Intestine Small	intestine

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