Variant report

Variant	rs826854
Chromosome Location	chr12:39114669-39114670
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:93)

rs_ID	r²[population]
rs10160990	0.80[EUR][1000 genomes]
rs1095573	0.82[EUR][1000 genomes]
rs1095576	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168929	0.87[AMR][1000 genomes]
rs11169037	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11169056	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11169105	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11169268	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169324	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169615	0.84[EUR][1000 genomes]
rs11169618	0.84[EUR][1000 genomes]
rs11537523	0.80[EUR][1000 genomes]
rs11559976	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12231800	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1486342	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1486343	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1486355	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1523119	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1523120	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1533918	0.80[EUR][1000 genomes]
rs1615648	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1621487	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1684397	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1719833	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1719847	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1719860	0.80[EUR][1000 genomes]
rs1996879	0.80[EUR][1000 genomes]
rs2069210	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2134398	0.83[AMR][1000 genomes]
rs2455609	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2455610	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2630776	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2630778	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2630780	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2630782	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2653722	0.80[EUR][1000 genomes]
rs2653738	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2653752	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2653754	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2653760	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2653761	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2653769	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2653775	0.83[AMR][1000 genomes]
rs2730897	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2730901	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2730907	0.82[AMR][1000 genomes]
rs2730908	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2730909	0.80[AMR][1000 genomes]
rs2730944	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2730946	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2730948	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2730949	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2730954	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2730955	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2730957	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2730964	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4494337	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60368384	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs68075931	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73269131	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8181763	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8181765	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs826839	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs826840	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs826841	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs826845	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826846	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs826847	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826849	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs826853	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826857	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826860	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs826861	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826862	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826865	0.92[ASN][1000 genomes]
rs826866	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs826867	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826868	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826869	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs826871	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826872	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826880	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826884	0.84[EUR][1000 genomes]
rs826885	0.85[EUR][1000 genomes]
rs826887	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826890	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs826894	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs826895	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs826896	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs851933	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs862331	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs862332	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs866120	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39056000-39114800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:39056000-39168600	Weak transcription	Hela-S3	cervix
3	chr12:39080600-39115600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:39092600-39153600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:39095800-39117800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:39109800-39116800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:39110800-39119800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:39111000-39115600	Weak transcription	GM12878-XiMat	blood
9	chr12:39111400-39115200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr12:39111800-39119400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr12:39112400-39115200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr12:39112400-39118400	Weak transcription	Fetal Intestine Small	intestine
13	chr12:39113000-39114800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr12:39113000-39117200	Weak transcription	Colonic Mucosa	Colon
15	chr12:39113200-39114800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr12:39113200-39116000	Strong transcription	Left Ventricle	heart
17	chr12:39113400-39115400	Weak transcription	Ovary	ovary
18	chr12:39113800-39115400	Weak transcription	Fetal Intestine Large	intestine
19	chr12:39113800-39117000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:39113800-39117600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:39113800-39118400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:39113800-39123800	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr12:39114000-39115600	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:39114000-39115800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:39114000-39115800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:39114000-39117200	Weak transcription	Fetal Stomach	stomach
27	chr12:39114000-39118400	Strong transcription	Liver	Liver
28	chr12:39114200-39115800	Strong transcription	Right Ventricle	heart
29	chr12:39114200-39133600	Weak transcription	A549	lung
30	chr12:39114400-39114800	Strong transcription	Lung	lung
31	chr12:39114400-39115600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:39114400-39115600	Strong transcription	Pancreas	Pancrea
33	chr12:39114400-39116000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:39114400-39116000	Strong transcription	Aorta	Aorta
35	chr12:39114400-39124800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:39114600-39115400	Strong transcription	Spleen	Spleen
37	chr12:39114600-39115800	ZNF genes & repeats	Gastric	stomach
38	chr12:39114600-39116000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:39114600-39116000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:39114600-39116400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr12:39114600-39116400	Strong transcription	Esophagus	oesophagus
42	chr12:39114600-39116400	Strong transcription	Stomach Smooth Muscle	stomach
43	chr12:39114600-39116800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr12:39114600-39117000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:39114600-39117600	Strong transcription	Adipose Nuclei	Adipose

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