Variant report

Variant	rs6034539
Chromosome Location	chr20:16560330-16560331
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:16554484..16557263-chr20:16559352..16563570,6	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1007144	0.85[AMR][1000 genomes]
rs13042615	0.88[EUR][1000 genomes]
rs13044683	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2179905	0.96[EUR][1000 genomes]
rs2328045	0.98[EUR][1000 genomes]
rs34548254	0.98[EUR][1000 genomes]
rs34678561	0.96[EUR][1000 genomes]
rs35610860	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4813225	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55776240	0.98[EUR][1000 genomes]
rs6034535	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6044121	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6044124	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6044128	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6044141	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6044146	0.95[EUR][1000 genomes]
rs6105631	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6111190	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6111195	0.96[EUR][1000 genomes]
rs6514692	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6514693	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs926772	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs926773	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs997972	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	esv2762064	chr20:16558260-16568062	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
2	nsv1058496	chr20:16558260-16575531	Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6034539	KIF16B	cis	Whole Blood	GTEx
rs6034539	C20orf23	Cis_1M	lymphoblastoid	RTeQTL
rs6034539	KIF16B	cis	Thyroid	GTEx
rs6034539	KIF16B	cis	Muscle Skeletal	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16556200-16560400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr20:16556400-16560800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr20:16556400-16560800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr20:16556400-16561000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr20:16556400-16562400	Weak transcription	Left Ventricle	heart
6	chr20:16556600-16560400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr20:16556600-16560600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr20:16556600-16560600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr20:16556600-16560600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr20:16556600-16560800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr20:16556600-16560800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr20:16556600-16560800	Weak transcription	Adipose Nuclei	Adipose
13	chr20:16556600-16560800	Weak transcription	Colon Smooth Muscle	Colon
14	chr20:16556600-16560800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr20:16556600-16561000	Weak transcription	Colonic Mucosa	Colon
16	chr20:16556800-16560800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr20:16556800-16560800	Weak transcription	Fetal Brain Female	brain
18	chr20:16556800-16560800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr20:16557000-16560600	Weak transcription	A549	lung
20	chr20:16557000-16561000	Weak transcription	Fetal Muscle Leg	muscle
21	chr20:16557200-16560600	Weak transcription	HepG2	liver
22	chr20:16559400-16560400	Enhancers	Pancreas	Pancrea
23	chr20:16559400-16562000	Enhancers	Fetal Intestine Large	intestine
24	chr20:16559600-16560400	Enhancers	Esophagus	oesophagus
25	chr20:16559600-16560400	Enhancers	Gastric	stomach
26	chr20:16559600-16560400	Enhancers	Lung	lung
27	chr20:16559600-16561200	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr20:16559600-16561800	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr20:16559600-16561800	Enhancers	NHDF-Ad	bronchial
30	chr20:16559600-16562000	Enhancers	Duodenum Mucosa	Duodenum
31	chr20:16559600-16562000	Enhancers	Fetal Intestine Small	intestine
32	chr20:16559600-16562200	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr20:16559800-16561000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr20:16559800-16562000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr20:16559800-16562200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr20:16559800-16564600	Enhancers	Fetal Brain Male	brain
37	chr20:16559800-16567000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr20:16560000-16560800	Enhancers	Fetal Kidney	kidney
39	chr20:16560000-16561200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr20:16560000-16561400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr20:16560000-16561600	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr20:16560000-16561600	Enhancers	HMEC	breast
43	chr20:16560000-16561800	Enhancers	Osteobl	bone
44	chr20:16560000-16562000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr20:16560000-16562000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr20:16560000-16562000	Enhancers	Stomach Mucosa	stomach
47	chr20:16560000-16562200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr20:16560000-16562200	Enhancers	NHEK	skin
49	chr20:16560000-16562400	Enhancers	Placenta Amnion	Placenta Amnion
50	chr20:16560000-16562600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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