Variant report

Variant	rs262033
Chromosome Location	chr5:178020475-178020476
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10063148	0.82[ASN][1000 genomes]
rs10066600	0.82[ASN][1000 genomes]
rs10070146	0.82[ASN][1000 genomes]
rs10464070	0.87[ASN][1000 genomes]
rs10479431	0.83[ASN][1000 genomes]
rs11747899	0.80[EUR][1000 genomes]
rs12054903	0.82[ASN][1000 genomes]
rs12234109	1.00[ASN][1000 genomes]
rs13181921	0.91[ASN][1000 genomes]
rs262023	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs262024	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs262029	0.89[ASN][1000 genomes]
rs262041	0.90[ASN][1000 genomes]
rs262042	0.91[ASN][1000 genomes]
rs34183525	0.95[ASN][1000 genomes]
rs34724127	0.82[ASN][1000 genomes]
rs540371	0.91[ASN][1000 genomes]
rs543862	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55724549	0.85[ASN][1000 genomes]
rs55783860	0.83[ASN][1000 genomes]
rs57862544	0.91[ASN][1000 genomes]
rs62392801	0.83[ASN][1000 genomes]
rs6884172	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6884657	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71611451	0.82[ASN][1000 genomes]
rs71611452	0.82[ASN][1000 genomes]
rs7447517	0.98[ASN][1000 genomes]
rs7700943	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7724406	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[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
rs262033	CLK4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178017600-178021000	Weak transcription	Spleen	Spleen
2	chr5:178017800-178021000	Weak transcription	Lung	lung
3	chr5:178017800-178021200	Weak transcription	Ovary	ovary
4	chr5:178017800-178023200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:178017800-178031400	Weak transcription	Pancreas	Pancrea
6	chr5:178017800-178033400	Weak transcription	Esophagus	oesophagus
7	chr5:178017800-178033400	Weak transcription	Gastric	stomach
8	chr5:178017800-178033400	Weak transcription	Right Atrium	heart
9	chr5:178018000-178021200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr5:178018000-178021200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr5:178018000-178021200	Weak transcription	HSMM	muscle
12	chr5:178018000-178026400	Weak transcription	Placenta	Placenta
13	chr5:178018000-178028600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:178018200-178021200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:178018200-178021200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr5:178018200-178021400	Weak transcription	Brain Substantia Nigra	brain
17	chr5:178018200-178021400	Weak transcription	Colon Smooth Muscle	Colon
18	chr5:178018200-178021800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:178018200-178022000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:178018200-178022200	Weak transcription	Liver	Liver
21	chr5:178018200-178030000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr5:178018200-178032600	Weak transcription	Brain Angular Gyrus	brain
23	chr5:178018200-178043200	Weak transcription	Aorta	Aorta
24	chr5:178018400-178020800	Weak transcription	Fetal Stomach	stomach
25	chr5:178018400-178023000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr5:178018400-178024200	Weak transcription	Osteobl	bone
27	chr5:178018400-178029600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr5:178018600-178021400	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr5:178018600-178021800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:178018600-178022000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr5:178018600-178026400	Weak transcription	HSMMtube	muscle
32	chr5:178018600-178030000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr5:178018800-178021200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr5:178018800-178021200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr5:178018800-178022200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:178018800-178024600	Weak transcription	Left Ventricle	heart
37	chr5:178019000-178022200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr5:178019000-178022400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:178019000-178029600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr5:178019000-178031400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:178019200-178021800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr5:178019200-178024200	Weak transcription	Fetal Thymus	thymus
43	chr5:178019400-178036800	Weak transcription	Psoas Muscle	Psoas
44	chr5:178019600-178021000	Weak transcription	Fetal Muscle Leg	muscle
45	chr5:178019600-178027200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr5:178020000-178021000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr5:178020400-178021200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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