Variant report

Variant	rs61839602
Chromosome Location	chr1:223012488-223012489
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	chr1:222996626..222998814-chr1:223011905..223014291,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228106	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10495202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1132369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1132371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588378	0.86[AMR][1000 genomes]
rs12734196	0.95[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17475431	0.93[EUR][1000 genomes]
rs17475753	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17475774	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17476063	0.87[ASN][1000 genomes]
rs17477752	0.86[AMR][1000 genomes]
rs17534704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17534774	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17535004	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17535032	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17535137	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17535305	0.81[ASN][1000 genomes]
rs17536056	0.91[AMR][1000 genomes]
rs17536209	0.91[AMR][1000 genomes]
rs17536299	0.91[AMR][1000 genomes]
rs17536396	0.91[AMR][1000 genomes]
rs17536522	0.86[AMR][1000 genomes]
rs34074917	0.81[ASN][1000 genomes]
rs34080450	0.82[AMR][1000 genomes]
rs34096996	0.92[EUR][1000 genomes]
rs34139393	0.92[EUR][1000 genomes]
rs34151467	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34194482	0.95[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs34225287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34229647	0.94[EUR][1000 genomes]
rs34232799	0.82[AMR][1000 genomes]
rs34277924	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34299243	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34300028	0.91[EUR][1000 genomes]
rs34355153	0.86[AMR][1000 genomes]
rs34503525	0.86[AMR][1000 genomes]
rs34505570	0.93[EUR][1000 genomes]
rs34643369	0.91[AMR][1000 genomes]
rs34651530	0.81[EUR][1000 genomes]
rs34682656	0.81[ASN][1000 genomes]
rs34690779	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34701716	0.82[AMR][1000 genomes]
rs34713681	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34755094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34761499	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34764163	0.81[ASN][1000 genomes]
rs34774807	0.86[AMR][1000 genomes]
rs34791822	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34804073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34873092	0.81[ASN][1000 genomes]
rs34893395	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34898792	0.92[EUR][1000 genomes]
rs34950986	0.93[EUR][1000 genomes]
rs34962524	0.95[AMR][1000 genomes]
rs34984199	0.81[ASN][1000 genomes]
rs35131473	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35197173	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35217299	0.82[AMR][1000 genomes]
rs35270311	0.95[EUR][1000 genomes]
rs35270996	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35283922	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35319605	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35356885	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35399857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35497286	0.93[EUR][1000 genomes]
rs35506390	0.86[AMR][1000 genomes]
rs35538644	0.86[AMR][1000 genomes]
rs35578837	0.91[AMR][1000 genomes]
rs35591569	0.93[EUR][1000 genomes]
rs35597626	0.86[AMR][1000 genomes]
rs35597790	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35689138	0.86[AMR][1000 genomes]
rs35756512	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35773347	0.91[AMR][1000 genomes]
rs35787799	0.93[EUR][1000 genomes]
rs35898924	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35912520	0.91[AMR][1000 genomes]
rs35947021	0.82[AMR][1000 genomes]
rs35979308	0.81[ASN][1000 genomes]
rs36032255	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs36044931	0.81[ASN][1000 genomes]
rs36066427	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs36090356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36113407	0.95[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4298738	0.86[AMR][1000 genomes]
rs61838099	0.86[EUR][1000 genomes]
rs61838105	0.93[EUR][1000 genomes]
rs61838107	0.92[EUR][1000 genomes]
rs61838113	0.95[EUR][1000 genomes]
rs61838115	0.95[EUR][1000 genomes]
rs61838118	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61838119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61839587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61839588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61839600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61839601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61840263	0.95[AMR][1000 genomes]
rs61840265	0.81[ASN][1000 genomes]
rs61840271	0.86[AMR][1000 genomes]
rs61840273	0.86[AMR][1000 genomes]
rs66597772	0.81[ASN][1000 genomes]
rs71644708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71644709	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71644714	0.86[AMR][1000 genomes]
rs71644716	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs71644718	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv873206	chr1:222985197-223124916	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222989400-223026800	Weak transcription	Fetal Muscle Leg	muscle
2	chr1:222990400-223027400	Weak transcription	Primary B cells from cord blood	blood
3	chr1:222991800-223017200	Weak transcription	Aorta	Aorta
4	chr1:222997000-223016600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:222999600-223015600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:223002200-223017000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:223002600-223019800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:223003600-223013400	Weak transcription	Fetal Stomach	stomach
9	chr1:223007200-223017200	Weak transcription	Fetal Lung	lung
10	chr1:223007400-223016200	Weak transcription	Fetal Intestine Large	intestine
11	chr1:223007800-223016200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:223007800-223016800	Weak transcription	Fetal Intestine Small	intestine
13	chr1:223007800-223017400	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:223008000-223017000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:223008200-223013400	Weak transcription	HSMMtube	muscle
16	chr1:223010000-223015200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:223010800-223015800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:223010800-223027600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr1:223012200-223013000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:223012400-223012800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
21	chr1:223012400-223012800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:223012400-223012800	Enhancers	Gastric	stomach
23	chr1:223012400-223013600	Weak transcription	Fetal Muscle Trunk	muscle

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