Variant report

Variant	rs62153900
Chromosome Location	chr2:96977284-96977285
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:96969385..96974489-chr2:96975844..96980987,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144028	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1044594	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1048675	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11903461	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17420101	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17479466	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17633463	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2276648	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2276649	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2279105	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3171927	0.99[ASN][1000 genomes]
rs3214058	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3214063	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3731930	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3731935	0.81[ASN][1000 genomes]
rs3731936	0.81[ASN][1000 genomes]
rs4907231	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4907232	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4907307	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4907308	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4907309	0.84[AMR][1000 genomes]
rs4907310	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4907311	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4907312	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56027554	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56800261	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57406815	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58328293	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59966106	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59979953	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62153033	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62153034	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62153035	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62153039	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62153041	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62153898	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62153901	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62153902	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62153905	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62153906	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62153915	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62153923	0.81[AMR][1000 genomes]
rs6755877	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7562544	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
9	nsv508155	chr2:96934695-97138302	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs62153900	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs62153900	CIAO1	cis	Esophagus Mucosa	GTEx
rs62153900	AC008268.2	cis	Thyroid	GTEx
rs62153900	AC008268.2	cis	Heart Left Ventricle	GTEx
rs62153900	AC008268.2	cis	lung	GTEx
rs62153900	AC008268.2	cis	Skin Sun Exposed Lower leg	GTEx
rs62153900	AC008268.2	cis	Artery Tibial	GTEx
rs62153900	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx
rs62153900	CIAO1	Cis_1M	lymphoblastoid	RTeQTL
rs62153900	CIAO1	cis	Adipose Subcutaneous	GTEx
rs62153900	AC008268.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96972400-96980200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr2:96972400-96980400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:96972400-96980800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:96972400-96981200	Weak transcription	Thymus	Thymus
5	chr2:96972400-96981600	Weak transcription	Primary B cells from cord blood	blood
6	chr2:96972600-96980400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:96972600-96980800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr2:96972600-96980800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:96972600-96980800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr2:96972600-96980800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:96972600-96981000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr2:96974400-96978200	Weak transcription	K562	blood
13	chr2:96976000-96980800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr2:96976200-96979000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:96977000-96978800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links