Variant report

Variant	rs62445924
Chromosome Location	chr7:21959378-21959379
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10950883	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1128250	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12055905	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12055908	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12539984	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12673256	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1919906	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55658106	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57033293	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57082026	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59258063	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62445926	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62445928	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62445933	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6959493	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6959806	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6963571	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6978094	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7798564	0.86[EUR][1000 genomes]
rs7807924	0.89[AMR][1000 genomes];0.93[EUR][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	nsv1018133	chr7:21740118-22055283	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv830922	chr7:21793386-21964675	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1027453	chr7:21918474-21982448	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62445924	CDCA7L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21933000-21963200	Weak transcription	A549	lung
2	chr7:21938600-21984000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:21946200-21963400	Weak transcription	Brain Hippocampus Middle	brain
4	chr7:21948400-21960400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr7:21948800-21981000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:21950400-21960400	Weak transcription	Fetal Brain Female	brain
7	chr7:21951600-21982600	Weak transcription	HSMM	muscle
8	chr7:21952400-21963200	Weak transcription	Psoas Muscle	Psoas
9	chr7:21952600-21977400	Weak transcription	NHDF-Ad	bronchial
10	chr7:21952800-21960000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr7:21952800-21963200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr7:21953400-21960200	Weak transcription	Brain Germinal Matrix	brain
13	chr7:21954400-21960400	Weak transcription	Brain Anterior Caudate	brain
14	chr7:21954400-21963200	Weak transcription	Hela-S3	cervix
15	chr7:21954800-21961800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr7:21954800-21962800	Weak transcription	Pancreas	Pancrea
17	chr7:21954800-21966200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:21954800-21970400	Weak transcription	Liver	Liver
19	chr7:21954800-21971800	Weak transcription	Gastric	stomach
20	chr7:21955000-21959600	Weak transcription	GM12878-XiMat	blood
21	chr7:21955000-21960400	Weak transcription	Right Ventricle	heart
22	chr7:21955000-21967400	Weak transcription	Fetal Intestine Small	intestine
23	chr7:21955000-21969800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr7:21955000-21979000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr7:21955000-21979200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr7:21955000-21979600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr7:21955000-21981000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr7:21955200-21967800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr7:21955800-21960200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:21956000-21959400	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr7:21956000-21960200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr7:21956000-21961600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr7:21956000-21961600	Weak transcription	HUVEC	blood vessel
34	chr7:21956000-21966200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr7:21956000-21976400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr7:21956000-21981000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr7:21956200-21961800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr7:21956200-21962800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr7:21956200-21963000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr7:21956200-21963200	Weak transcription	Ovary	ovary
41	chr7:21956200-21967200	Weak transcription	Thymus	Thymus
42	chr7:21956200-21967400	Weak transcription	Fetal Stomach	stomach
43	chr7:21956200-21976800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr7:21956400-21959800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr7:21956400-21959800	Weak transcription	Fetal Lung	lung
46	chr7:21956400-21960000	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr7:21956400-21961400	Weak transcription	Adipose Nuclei	Adipose
48	chr7:21956400-21965400	Enhancers	Fetal Heart	heart
49	chr7:21956400-21980200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr7:21956600-21959400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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