Variant report

Variant	rs7954990
Chromosome Location	chr12:29452774-29452775
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10450679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052583	0.87[EUR][1000 genomes]
rs10743651	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10743652	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10843365	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10843372	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10843402	0.82[ASN][1000 genomes]
rs11050200	0.87[EUR][1000 genomes]
rs1120528	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1991113	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2059362	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2194517	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2882294	0.84[EUR][1000 genomes]
rs3782507	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3782508	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4370971	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4412790	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6487789	0.81[EUR][1000 genomes]
rs6487791	0.86[EUR][1000 genomes]
rs6487792	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6487795	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6487797	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6487799	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6487800	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6487802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137141	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7295056	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7295212	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7299648	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7299772	0.82[EUR][1000 genomes]
rs7300032	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7301575	0.83[AMR][1000 genomes]
rs7302399	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7303960	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73063614	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7311081	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7316026	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs766445	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7954375	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7968167	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968883	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7971296	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7972032	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7974254	0.85[EUR][1000 genomes]
rs7976227	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7976667	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9669514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9738165	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29417200-29465400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr12:29422000-29455600	Weak transcription	Left Ventricle	heart
3	chr12:29422000-29465000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:29426800-29472800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
6	chr12:29429000-29460200	Weak transcription	Primary T cells from cord blood	blood
7	chr12:29429200-29463600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:29429400-29460400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr12:29435400-29467200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:29439600-29464000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:29439600-29469400	Weak transcription	NH-A	brain
12	chr12:29443400-29460200	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr12:29446200-29465000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr12:29448800-29456400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:29449600-29470800	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr12:29451600-29453200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:29451600-29453200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:29452000-29457800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr12:29452200-29452800	Enhancers	Primary hematopoietic stem cells	blood
20	chr12:29452200-29453000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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