Variant report

Variant	rs1989478
Chromosome Location	chr12:29442229-29442230
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10047562	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10743657	0.90[ASN][1000 genomes]
rs10743658	0.90[ASN][1000 genomes]
rs10771507	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10771508	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10843361	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10843366	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10843367	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10843371	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10843373	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10843375	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10843377	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10843382	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10843384	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10843398	0.90[ASN][1000 genomes]
rs11050151	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11050152	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11050153	0.84[EUR][1000 genomes]
rs11050157	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11050161	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11050162	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11050163	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11050167	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11050170	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11050181	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11050187	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11050188	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11050189	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11050191	0.81[AFR][1000 genomes]
rs11050192	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs11050193	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11050194	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11833737	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12228468	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12231498	0.83[EUR][1000 genomes]
rs12366505	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12366527	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16934135	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2042511	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2194518	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2194519	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2194520	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2216853	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2216854	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2278094	0.90[ASN][1000 genomes]
rs3764953	0.84[EUR][1000 genomes]
rs3782506	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3782509	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3782511	0.80[EUR][1000 genomes]
rs4331146	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4931177	0.88[ASN][1000 genomes]
rs4931178	0.88[ASN][1000 genomes]
rs57803026	0.85[EUR][1000 genomes]
rs6487790	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6487796	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6487801	0.83[AMR][1000 genomes]
rs6487804	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6487805	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6487808	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6487813	0.81[ASN][1000 genomes]
rs6487815	0.90[ASN][1000 genomes]
rs67146951	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67150462	0.81[AMR][1000 genomes]
rs67517901	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7131987	0.87[EUR][1000 genomes]
rs7139273	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7294598	0.82[EUR][1000 genomes]
rs7299861	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7301188	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7302129	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7302557	0.90[ASN][1000 genomes]
rs7308125	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7311912	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7312164	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7315504	0.90[ASN][1000 genomes]
rs7316004	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs737160	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7954278	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7954871	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7957339	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7958210	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7970390	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7973786	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7974221	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7976961	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs918873	0.82[AMR][1000 genomes]
rs962866	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9738721	0.81[AMR][1000 genomes];0.86[EUR][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:18 , 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	chr12:29427000-29452200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
7	chr12:29429000-29460200	Weak transcription	Primary T cells from cord blood	blood
8	chr12:29429200-29463600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr12:29429400-29460400	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr12:29432200-29442800	Weak transcription	Psoas Muscle	Psoas
11	chr12:29432800-29445800	Weak transcription	Primary B cells from cord blood	blood
12	chr12:29434200-29449600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr12:29435400-29467200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:29436400-29443200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:29437600-29451600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr12:29439600-29464000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:29439600-29469400	Weak transcription	NH-A	brain
18	chr12:29442000-29443800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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