Variant report

Variant	rs7447517
Chromosome Location	chr5:178021885-178021886
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr5:178021629-178023092	K562	blood:	n/a	n/a
2	KAP1	chr5:178021677-178023379	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178019997..178022007-chr5:178050984..178053956,2	MCF-7	breast:

Variant related genes	Relation type
COL23A1	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10063148	0.81[ASN][1000 genomes]
rs10066600	0.81[ASN][1000 genomes]
rs10070146	0.81[ASN][1000 genomes]
rs10464070	0.86[ASN][1000 genomes]
rs10479431	0.82[ASN][1000 genomes]
rs12054903	0.81[ASN][1000 genomes]
rs12234109	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13181921	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs262023	0.95[ASN][1000 genomes]
rs262024	0.97[ASN][1000 genomes]
rs262029	0.88[ASN][1000 genomes]
rs262033	0.98[ASN][1000 genomes]
rs262041	0.88[ASN][1000 genomes]
rs262042	0.89[ASN][1000 genomes]
rs34183525	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34724127	0.81[ASN][1000 genomes]
rs540371	0.89[ASN][1000 genomes]
rs543862	0.95[ASN][1000 genomes]
rs55724549	0.84[ASN][1000 genomes]
rs55783860	0.82[ASN][1000 genomes]
rs57862544	0.90[ASN][1000 genomes]
rs62392801	0.82[ASN][1000 genomes]
rs6884172	0.90[ASN][1000 genomes]
rs6884657	0.90[ASN][1000 genomes]
rs71611451	0.81[ASN][1000 genomes]
rs71611452	0.81[ASN][1000 genomes]
rs7700943	0.94[ASN][1000 genomes]
rs7724406	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv883214	chr5:177876309-178047217	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv883216	chr5:178002325-178025087	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7447517	CLK4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178017800-178023200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:178017800-178031400	Weak transcription	Pancreas	Pancrea
3	chr5:178017800-178033400	Weak transcription	Esophagus	oesophagus
4	chr5:178017800-178033400	Weak transcription	Gastric	stomach
5	chr5:178017800-178033400	Weak transcription	Right Atrium	heart
6	chr5:178018000-178026400	Weak transcription	Placenta	Placenta
7	chr5:178018000-178028600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:178018200-178022000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr5:178018200-178022200	Weak transcription	Liver	Liver
10	chr5:178018200-178030000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr5:178018200-178032600	Weak transcription	Brain Angular Gyrus	brain
12	chr5:178018200-178043200	Weak transcription	Aorta	Aorta
13	chr5:178018400-178023000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:178018400-178024200	Weak transcription	Osteobl	bone
15	chr5:178018400-178029600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:178018600-178022000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr5:178018600-178026400	Weak transcription	HSMMtube	muscle
18	chr5:178018600-178030000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr5:178018800-178022200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:178018800-178024600	Weak transcription	Left Ventricle	heart
21	chr5:178019000-178022200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr5:178019000-178022400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:178019000-178029600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr5:178019000-178031400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr5:178019200-178024200	Weak transcription	Fetal Thymus	thymus
26	chr5:178019400-178036800	Weak transcription	Psoas Muscle	Psoas
27	chr5:178019600-178027200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:178020600-178028000	Weak transcription	NHLF	lung
29	chr5:178021200-178023200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
30	chr5:178021200-178023600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
31	chr5:178021200-178024000	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr5:178021400-178022400	ZNF genes & repeats	Colon Smooth Muscle	Colon
33	chr5:178021400-178023200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
34	chr5:178021400-178024000	Weak transcription	Thymus	Thymus
35	chr5:178021400-178024400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:178021400-178024400	Weak transcription	Fetal Intestine Small	intestine
37	chr5:178021400-178024400	Weak transcription	Lung	lung
38	chr5:178021400-178025200	Weak transcription	Spleen	Spleen
39	chr5:178021600-178022800	Weak transcription	HSMM	muscle
40	chr5:178021600-178024000	Weak transcription	Fetal Stomach	stomach
41	chr5:178021600-178031200	Weak transcription	Ovary	ovary
42	chr5:178021800-178022800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
43	chr5:178021800-178023200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
44	chr5:178021800-178023200	ZNF genes & repeats	Fetal Lung	lung
45	chr5:178021800-178023600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr5:178021800-178024600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr5:178021800-178024600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr5:178021800-178026800	Weak transcription	A549	lung

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