Variant report

Variant	rs6078084
Chromosome Location	chr20:11151237-11151238
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11698972	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13036917	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13043918	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13044954	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2327339	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4813962	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6074259	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6074260	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6078088	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6078089	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6078090	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6078091	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6078093	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6078084	MED24	trans	cerebellum	SCAN
rs6078084	FLRT3	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:11148800-11152600	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr20:11149200-11152200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr20:11149600-11158800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr20:11150200-11151800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr20:11150400-11152200	Enhancers	Muscle Satellite Cultured Cells	--
6	chr20:11150600-11151800	Enhancers	Osteobl	bone
7	chr20:11150800-11151600	Enhancers	Fetal Kidney	kidney
8	chr20:11150800-11151600	Enhancers	NHDF-Ad	bronchial
9	chr20:11150800-11152000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr20:11150800-11152200	Enhancers	HSMMtube	muscle
11	chr20:11150800-11152800	Enhancers	HSMM	muscle
12	chr20:11151000-11151400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr20:11151000-11151400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr20:11151000-11151600	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr20:11151000-11151600	Enhancers	NH-A	brain
16	chr20:11151200-11151400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr20:11151200-11151400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr20:11151200-11151400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr20:11151200-11151400	Flanking Active TSS	HUVEC	blood vessel
20	chr20:11151200-11151600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr20:11151200-11151600	Enhancers	A549	lung
22	chr20:11151200-11151600	Enhancers	HMEC	breast
23	chr20:11151200-11151800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr20:11151200-11152200	Enhancers	NHEK	skin

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