Variant report

Variant	rs66514959
Chromosome Location	chr5:68611583-68611584
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10940215	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11745537	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11745591	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11749723	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11750525	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11957698	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12189282	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13154469	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13168973	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28499200	0.82[EUR][1000 genomes]
rs34449757	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34862981	0.82[EUR][1000 genomes]
rs35316810	0.84[EUR][1000 genomes]
rs35438259	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4288083	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs68083627	0.80[EUR][1000 genomes]
rs6865481	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6877725	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6881767	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6893648	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][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	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs66514959	CCDC125	cis	lung	GTEx
rs66514959	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx
rs66514959	CFL1P5	cis	Thyroid	GTEx
rs66514959	CCDC125	cis	Thyroid	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68541200-68620400	Weak transcription	Stomach Mucosa	stomach
2	chr5:68565600-68627400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr5:68576400-68614400	Weak transcription	Colon Smooth Muscle	Colon
4	chr5:68576400-68627600	Weak transcription	Brain Substantia Nigra	brain
5	chr5:68576400-68627800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr5:68576600-68627800	Weak transcription	Brain Angular Gyrus	brain
7	chr5:68577400-68628200	Weak transcription	Small Intestine	intestine
8	chr5:68577600-68619800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr5:68577600-68627400	Weak transcription	NHEK	skin
10	chr5:68577800-68626600	Weak transcription	A549	lung
11	chr5:68581600-68627600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:68581800-68617800	Weak transcription	Brain Hippocampus Middle	brain
13	chr5:68581800-68626800	Weak transcription	Fetal Brain Female	brain
14	chr5:68581800-68627600	Weak transcription	Brain Anterior Caudate	brain
15	chr5:68582800-68622400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:68588600-68615800	Weak transcription	Colonic Mucosa	Colon
17	chr5:68591600-68614000	Weak transcription	Osteobl	bone
18	chr5:68591600-68627600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:68596000-68626800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr5:68596600-68612800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr5:68599400-68612000	Weak transcription	HepG2	liver
22	chr5:68599600-68627800	Weak transcription	NH-A	brain
23	chr5:68601400-68627600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr5:68605600-68612000	Weak transcription	Ovary	ovary
25	chr5:68605600-68613800	Weak transcription	Brain Germinal Matrix	brain
26	chr5:68605600-68627400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr5:68606200-68625600	Weak transcription	Hela-S3	cervix
28	chr5:68607400-68612600	Strong transcription	Fetal Intestine Small	intestine
29	chr5:68608400-68613200	Weak transcription	Primary B cells from cord blood	blood
30	chr5:68609000-68612800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr5:68609000-68613200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr5:68609200-68612000	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr5:68609400-68622400	Weak transcription	K562	blood
34	chr5:68609600-68612000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr5:68609600-68613400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr5:68609600-68624000	Weak transcription	Placenta	Placenta
37	chr5:68609600-68627400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr5:68609600-68627600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr5:68609800-68611600	Weak transcription	NHLF	lung
40	chr5:68609800-68611800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:68609800-68612000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr5:68609800-68612000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr5:68609800-68612000	Weak transcription	Spleen	Spleen
44	chr5:68609800-68613800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr5:68609800-68615200	Weak transcription	Gastric	stomach
46	chr5:68609800-68615800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr5:68609800-68616000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr5:68609800-68617600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr5:68609800-68621000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr5:68609800-68621000	Weak transcription	Thymus	Thymus

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