Variant report

Variant	rs12523580
Chromosome Location	chr3:143516854-143516855
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10463169	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10476669	0.81[ASN][1000 genomes]
rs10866766	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11135447	0.99[ASN][1000 genomes]
rs11135448	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11135449	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11135451	0.91[ASN][1000 genomes]
rs11742368	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11742915	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11749674	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12519062	0.97[ASN][1000 genomes]
rs12652939	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12652970	0.82[ASN][1000 genomes]
rs12653663	0.81[ASN][1000 genomes]
rs12659174	0.82[ASN][1000 genomes]
rs13173638	0.82[AMR][1000 genomes]
rs13183250	0.97[ASN][1000 genomes]
rs13358858	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3922469	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4077817	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4301244	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4492136	0.82[ASN][1000 genomes]
rs4569897	0.82[ASN][1000 genomes]
rs4626359	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56699153	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs59090200	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59238624	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61618257	0.81[ASN][1000 genomes]
rs6556909	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6862359	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6877002	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6877070	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6877397	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6878441	0.82[AMR][1000 genomes]
rs6880865	0.81[ASN][1000 genomes]
rs6883290	0.87[ASN][1000 genomes]
rs6895145	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6895197	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6895503	0.81[ASN][1000 genomes]
rs6895664	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73138312	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73138313	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73138318	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73138324	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73138336	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73138348	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73138350	0.94[ASN][1000 genomes]
rs73138358	0.91[ASN][1000 genomes]
rs73138366	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73138380	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7700756	0.82[AMR][1000 genomes]
rs7701835	0.82[AMR][1000 genomes]
rs7706272	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7731306	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7734553	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7735346	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7735670	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv3418674	chr3:143457005-143558357	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1009935	chr3:143497700-143610852	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1001076	chr3:143513526-143547076	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv536747	chr3:143513526-143547076	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143505800-143525800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:143506000-143521200	Weak transcription	Primary B cells from peripheral blood	blood
3	chr3:143512000-143529200	Weak transcription	Primary B cells from cord blood	blood
4	chr3:143513400-143517400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:143513600-143533600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr3:143513800-143517800	Weak transcription	Fetal Stomach	stomach
7	chr3:143513800-143525800	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:143514000-143524200	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr3:143514000-143527400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:143514200-143519800	Weak transcription	HSMMtube	muscle
11	chr3:143514200-143544200	Weak transcription	Primary T cells from cord blood	blood
12	chr3:143514600-143517000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:143515000-143517600	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr3:143515000-143517600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:143515000-143522200	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr3:143516800-143517600	Enhancers	HSMM	muscle

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