Variant report

Variant	rs826847
Chromosome Location	chr12:39153088-39153089
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10160990	0.89[EUR][1000 genomes]
rs1095573	0.91[EUR][1000 genomes]
rs1095576	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1095578	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11168929	0.87[AMR][1000 genomes]
rs11169037	0.90[AMR][1000 genomes]
rs11169056	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11169105	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11169268	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169324	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169604	0.89[AFR][1000 genomes]
rs11169615	0.89[EUR][1000 genomes]
rs11169618	0.89[EUR][1000 genomes]
rs11537523	0.89[EUR][1000 genomes]
rs11559976	0.86[AMR][1000 genomes]
rs12231800	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1400281	0.82[EUR][1000 genomes]
rs1486342	0.94[AMR][1000 genomes]
rs1486343	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1486355	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1523119	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1523120	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1533917	0.82[EUR][1000 genomes]
rs1533918	0.89[EUR][1000 genomes]
rs1615648	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1621487	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1684397	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1684405	0.82[AMR][1000 genomes]
rs1684426	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1719833	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1719847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1719860	0.86[EUR][1000 genomes]
rs1996879	0.89[EUR][1000 genomes]
rs2056529	0.82[EUR][1000 genomes]
rs2069210	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2455609	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2455610	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2630776	0.94[AMR][1000 genomes]
rs2630778	0.90[AMR][1000 genomes]
rs2630780	0.94[AMR][1000 genomes]
rs2630782	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2653738	0.84[AMR][1000 genomes]
rs2653752	0.82[AMR][1000 genomes]
rs2653754	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2653760	0.90[AMR][1000 genomes]
rs2653761	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2653769	0.89[AMR][1000 genomes]
rs2730944	0.82[AMR][1000 genomes]
rs2730946	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2730948	0.94[AMR][1000 genomes]
rs2730949	0.94[AMR][1000 genomes]
rs2730954	0.90[AMR][1000 genomes]
rs2730955	0.94[AMR][1000 genomes]
rs2730957	0.94[AMR][1000 genomes]
rs2730964	0.84[AMR][1000 genomes]
rs4002228	0.88[EUR][1000 genomes]
rs4494337	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4768394	0.82[EUR][1000 genomes]
rs60368384	0.94[AMR][1000 genomes]
rs68075931	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7298168	0.82[EUR][1000 genomes]
rs73269131	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8181763	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8181765	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs826839	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs826840	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs826841	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs826845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826846	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs826849	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs826853	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826854	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826857	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826860	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs826861	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826862	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826863	0.82[AMR][1000 genomes]
rs826865	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs826866	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs826867	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826868	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826869	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs826871	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826872	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826880	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs826882	0.93[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs826884	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs826885	0.91[EUR][1000 genomes]
rs826887	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs826890	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs826894	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs826895	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs826896	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs851933	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs862331	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs862332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs866120	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[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	nsv469356	chr12:38242029-39187408	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv558574	chr12:38242029-39187408	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv1039538	chr12:38640895-39180750	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39056000-39168600	Weak transcription	Hela-S3	cervix
2	chr12:39092600-39153600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:39115800-39164400	Weak transcription	Lung	lung
4	chr12:39116000-39154800	Weak transcription	Aorta	Aorta
5	chr12:39118400-39165600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:39135800-39159000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:39139000-39153600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:39140600-39155000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:39141000-39155800	Weak transcription	Ovary	ovary
10	chr12:39141800-39153600	Weak transcription	Adipose Nuclei	Adipose
11	chr12:39142400-39154200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:39143800-39153200	Weak transcription	Liver	Liver
13	chr12:39144200-39163400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:39144200-39173800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:39144400-39153600	Weak transcription	Left Ventricle	heart
16	chr12:39144600-39156200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr12:39145000-39153200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:39146000-39153600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:39146400-39165400	Weak transcription	GM12878-XiMat	blood
20	chr12:39149400-39154800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:39149800-39155400	Weak transcription	Right Ventricle	heart
22	chr12:39150400-39154800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:39151400-39157800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:39152200-39158000	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr12:39152200-39161400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:39152200-39171400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:39152400-39155000	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr12:39152600-39165600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr12:39152800-39153200	Weak transcription	Fetal Brain Male	brain
30	chr12:39152800-39154600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:39152800-39165600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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