Variant report

Variant	rs12231800
Chromosome Location	chr12:39085869-39085870
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1095576	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168929	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11169037	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11169056	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11169105	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169268	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169324	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11559976	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1486342	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1486343	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1486355	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1523119	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1523120	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1615648	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1621487	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1684397	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1719833	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1719847	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2069210	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2455609	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2455610	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2630776	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2630778	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2630780	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2630782	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2653722	0.83[EUR][1000 genomes]
rs2653738	0.86[EUR][1000 genomes]
rs2653752	0.81[EUR][1000 genomes]
rs2653754	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2653760	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2653761	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2653769	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2730897	0.86[EUR][1000 genomes]
rs2730901	0.83[EUR][1000 genomes]
rs2730944	0.81[EUR][1000 genomes]
rs2730946	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2730948	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2730949	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2730954	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2730955	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2730957	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2730964	0.86[EUR][1000 genomes]
rs4494337	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60368384	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs68075931	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73269131	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8181763	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8181765	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs826839	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs826840	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs826841	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs826845	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs826846	0.82[ASN][1000 genomes]
rs826847	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs826849	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs826853	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs826854	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs826857	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs826860	0.84[ASN][1000 genomes]
rs826861	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs826862	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs826865	0.84[ASN][1000 genomes]
rs826866	0.84[ASN][1000 genomes]
rs826867	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs826868	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs826869	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs826871	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs826872	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs826880	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs826887	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs826890	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs826894	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs826895	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs826896	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs851933	0.81[ASN][1000 genomes]
rs862331	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs862332	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs866120	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
4	nsv1039821	chr12:38959645-39121578	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1053316	chr12:38959645-39122853	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1043831	chr12:38979065-39117868	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv541479	chr12:38979065-39117868	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39055800-39100800	Weak transcription	NHEK	skin
2	chr12:39056000-39092200	Weak transcription	Colon Smooth Muscle	Colon
3	chr12:39056000-39114800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:39056000-39168600	Weak transcription	Hela-S3	cervix
5	chr12:39066200-39114400	Weak transcription	Pancreas	Pancrea
6	chr12:39069400-39114600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr12:39074400-39098800	Weak transcription	Right Ventricle	heart
8	chr12:39079200-39114400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:39080600-39086600	Weak transcription	GM12878-XiMat	blood
10	chr12:39080600-39086800	Weak transcription	Ovary	ovary
11	chr12:39080600-39088600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:39080600-39089400	Weak transcription	A549	lung
13	chr12:39080600-39115600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr12:39080800-39086000	Strong transcription	Liver	Liver
15	chr12:39080800-39086800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:39080800-39087400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:39080800-39092400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr12:39080800-39094200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:39080800-39094200	Weak transcription	Lung	lung
20	chr12:39080800-39095800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr12:39080800-39096200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr12:39080800-39097400	Weak transcription	Fetal Intestine Small	intestine
23	chr12:39080800-39098600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr12:39080800-39105000	Weak transcription	Adipose Nuclei	Adipose
25	chr12:39081600-39087600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr12:39082800-39087800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr12:39083400-39113200	Weak transcription	Left Ventricle	heart
28	chr12:39084000-39091600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:39084200-39104800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:39085400-39086000	Strong transcription	Aorta	Aorta
31	chr12:39085600-39086200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:39085800-39086800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:39085800-39086800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:39085800-39088000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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