Variant report

Variant	rs12497109
Chromosome Location	chr3:157975176-157975177
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10513526	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10936130	0.90[EUR][1000 genomes]
rs12487397	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12487873	0.90[EUR][1000 genomes]
rs12490116	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12491983	0.89[EUR][1000 genomes]
rs12493633	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493753	0.89[EUR][1000 genomes]
rs12495621	0.85[EUR][1000 genomes]
rs12496739	0.87[EUR][1000 genomes]
rs12497273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631828	0.85[EUR][1000 genomes]
rs12631832	0.87[EUR][1000 genomes]
rs12634372	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12634405	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12634483	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12634966	0.90[EUR][1000 genomes]
rs12635395	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12635963	0.90[EUR][1000 genomes]
rs12637243	0.87[EUR][1000 genomes]
rs12637436	0.87[EUR][1000 genomes]
rs12638258	0.89[EUR][1000 genomes]
rs17486183	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17627838	0.89[EUR][1000 genomes]
rs17683721	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17683787	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2140982	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2176890	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2362247	0.85[EUR][1000 genomes]
rs28669117	0.84[EUR][1000 genomes]
rs28781280	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4021884	0.90[EUR][1000 genomes]
rs4432589	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55638807	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55818809	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56019559	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56101139	0.84[EUR][1000 genomes]
rs56130447	0.87[EUR][1000 genomes]
rs56303915	0.89[EUR][1000 genomes]
rs59661293	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60463398	0.83[EUR][1000 genomes]
rs60566034	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60921365	0.87[EUR][1000 genomes]
rs61244743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6762774	0.84[EUR][1000 genomes]
rs6769314	0.85[EUR][1000 genomes]
rs6804401	0.84[EUR][1000 genomes]
rs6806720	0.89[EUR][1000 genomes]
rs73166305	0.81[EUR][1000 genomes]
rs73166307	0.85[EUR][1000 genomes]
rs73166311	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73166326	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73166328	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73166334	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73166338	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73166343	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73166347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73166351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73166352	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73166357	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73166361	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73166362	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73166370	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73166374	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73166375	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73166381	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73166383	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73166386	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73166387	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73166388	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73166390	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73166394	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73166397	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73166399	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73168703	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73168704	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73168713	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73168718	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73168720	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73168737	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73170313	0.90[EUR][1000 genomes]
rs73170316	0.90[EUR][1000 genomes]
rs73170323	0.90[EUR][1000 genomes]
rs73170340	0.90[EUR][1000 genomes]
rs73170342	0.90[EUR][1000 genomes]
rs73170344	0.90[EUR][1000 genomes]
rs73170358	0.90[EUR][1000 genomes]
rs73170365	0.90[EUR][1000 genomes]
rs73170367	0.90[EUR][1000 genomes]
rs73170369	0.90[EUR][1000 genomes]
rs73170394	0.89[EUR][1000 genomes]
rs73170401	0.89[EUR][1000 genomes]
rs73172109	0.89[EUR][1000 genomes]
rs73172118	0.87[EUR][1000 genomes]
rs73172122	0.84[EUR][1000 genomes]
rs73172127	0.85[EUR][1000 genomes]
rs7650062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs951113	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9815348	0.84[EUR][1000 genomes]
rs9854620	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013391	chr3:157505943-158115553	Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv536775	chr3:157505943-158115553	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv829768	chr3:157832878-158012070	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv877689	chr3:157858930-158133307	Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv916910	chr3:157926799-158183372	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12497109	GFM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157914200-157984400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:157963800-157995800	Weak transcription	Gastric	stomach
3	chr3:157964600-157979600	Weak transcription	Small Intestine	intestine
4	chr3:157965800-157977400	Weak transcription	Ovary	ovary
5	chr3:157966000-157984600	Weak transcription	Left Ventricle	heart
6	chr3:157967600-157975400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:157969000-157979600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:157970600-157984400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr3:157971400-157977200	Weak transcription	Dnd41	blood
10	chr3:157971800-157977400	Weak transcription	Primary B cells from cord blood	blood
11	chr3:157972400-157978400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:157974200-157977600	Weak transcription	Primary T cells from cord blood	blood
13	chr3:157974800-157977200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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