Variant report

Variant	rs66604554
Chromosome Location	chr3:119276377-119276378
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	chr3:119272773..119276429-chr3:119297132..119299756,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272967	Chromatin interaction
ENSG00000144843	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10511393	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10934494	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11533815	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11543525	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12487080	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487334	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487335	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487430	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487965	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12489080	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12492723	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12494369	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12494451	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12495673	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496129	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496520	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496841	0.87[EUR][1000 genomes]
rs16829980	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16829988	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16830002	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16830004	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16830008	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1852212	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2019144	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2222630	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2222791	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34394661	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3915165	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3915166	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41271391	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41271393	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4330287	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4407429	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55668872	0.84[EUR][1000 genomes]
rs55702208	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55738731	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55758148	0.82[EUR][1000 genomes]
rs55772114	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55845727	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55848839	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55916342	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56025972	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56078908	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56086928	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56124423	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56135341	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56213221	0.82[EUR][1000 genomes]
rs58613639	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58924738	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59223102	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59374417	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59529797	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59639276	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59701395	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59762006	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59828023	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60920700	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61692996	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61702127	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6438537	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66797637	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66918189	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66920439	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67108211	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67160040	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67185025	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67212262	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67307954	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67369952	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67651191	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67765368	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68180496	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72953001	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73189896	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73189897	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73189899	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs762629	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs762631	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs867234	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs885654	0.93[EUR][1000 genomes];0.99[ASN][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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs66604554	CD80	cis	Muscle Skeletal	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119245200-119276600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr3:119267600-119298000	Weak transcription	Fetal Lung	lung
3	chr3:119271400-119281400	Weak transcription	Right Ventricle	heart
4	chr3:119272600-119276800	Enhancers	Primary B cells from peripheral blood	blood
5	chr3:119274800-119276600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:119274800-119278000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:119275000-119276400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr3:119275000-119276600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:119275000-119277800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:119275000-119277800	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr3:119275000-119278000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:119275000-119278000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:119275000-119278600	Weak transcription	Adipose Nuclei	Adipose
14	chr3:119275000-119278600	Weak transcription	Fetal Thymus	thymus
15	chr3:119275000-119281200	Weak transcription	Right Atrium	heart
16	chr3:119275000-119281200	Weak transcription	Spleen	Spleen
17	chr3:119275200-119276600	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr3:119275200-119277600	Weak transcription	Primary B cells from cord blood	blood
19	chr3:119275200-119278600	Active TSS	GM12878-XiMat	blood
20	chr3:119276000-119277200	Flanking Active TSS	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links