Variant report

Variant	rs6959493
Chromosome Location	chr7:21970781-21970782
allele	A/G
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];0.99[EUR][1000 genomes]
rs1128250	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12055905	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12055908	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12539984	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12673256	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1919906	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55658106	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57033293	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57082026	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59258063	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62445924	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62445926	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62445928	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62445933	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6959806	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6963571	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6978094	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7798564	0.89[EUR][1000 genomes]
rs7807924	0.93[AMR][1000 genomes];1.00[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	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
3	esv275068	chr7:21966107-21980773	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6959493	CDCA7L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21938600-21984000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:21948800-21981000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:21951600-21982600	Weak transcription	HSMM	muscle
4	chr7:21952600-21977400	Weak transcription	NHDF-Ad	bronchial
5	chr7:21954800-21971800	Weak transcription	Gastric	stomach
6	chr7:21955000-21979000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr7:21955000-21979200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:21955000-21979600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr7:21955000-21981000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr7:21956000-21976400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr7:21956000-21981000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr7:21956200-21976800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:21956400-21980200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr7:21956600-21983600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr7:21959800-21973800	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr7:21963400-21979200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr7:21963600-21983600	Weak transcription	Ovary	ovary
18	chr7:21964000-21979200	Weak transcription	Hela-S3	cervix
19	chr7:21964200-21977400	Weak transcription	HUVEC	blood vessel
20	chr7:21965000-21973600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr7:21965000-21976800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr7:21965200-21976400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr7:21965200-21982400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr7:21966400-21972200	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr7:21966600-21981000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr7:21967000-21977600	Weak transcription	NHEK	skin
27	chr7:21967600-21979000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr7:21967800-21971200	Weak transcription	Primary B cells from cord blood	blood
29	chr7:21967800-21971200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr7:21967800-21973400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr7:21967800-21974000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr7:21967800-21975400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr7:21967800-21976200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr7:21967800-21978000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr7:21967800-21978800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr7:21967800-21979200	Weak transcription	Thymus	Thymus
37	chr7:21967800-21979600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr7:21967800-21982000	Weak transcription	Fetal Stomach	stomach
39	chr7:21969800-21970800	Weak transcription	Primary T cells from cord blood	blood
40	chr7:21969800-21975800	Weak transcription	Fetal Lung	lung
41	chr7:21970400-21976600	Weak transcription	Fetal Thymus	thymus

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