Variant report

Variant	rs826893
Chromosome Location	chr12:39100536-39100537
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1021258	0.91[JPT][hapmap]
rs1038540	0.91[JPT][hapmap]
rs10747574	0.90[JPT][hapmap]
rs10875959	0.91[JPT][hapmap]
rs10875962	0.91[JPT][hapmap]
rs10875963	0.91[JPT][hapmap]
rs10875979	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs10875991	0.82[EUR][1000 genomes]
rs1095573	0.80[YRI][hapmap]
rs1095575	0.85[CEU][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1095577	0.91[JPT][hapmap]
rs11169095	0.88[JPT][hapmap]
rs11169142	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11169144	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11169169	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs11169301	0.80[EUR][1000 genomes]
rs11169407	0.91[JPT][hapmap]
rs12309958	0.91[JPT][hapmap]
rs12322306	0.85[EUR][1000 genomes]
rs1352122	0.86[EUR][1000 genomes]
rs1352123	0.84[EUR][1000 genomes]
rs1403523	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1486345	0.85[EUR][1000 genomes]
rs1486349	0.89[JPT][hapmap]
rs1486352	0.91[JPT][hapmap]
rs1486353	0.91[JPT][hapmap]
rs1486357	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs1615569	0.91[JPT][hapmap]
rs1615648	0.85[YRI][hapmap]
rs1619885	0.91[JPT][hapmap]
rs1620594	0.91[JPT][hapmap]
rs1620655	0.86[JPT][hapmap]
rs1624751	0.91[JPT][hapmap]
rs1684395	0.89[CEU][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1684406	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1684407	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1684411	0.85[EUR][1000 genomes]
rs1684413	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1684414	0.86[EUR][1000 genomes]
rs1684415	0.81[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1684416	0.83[EUR][1000 genomes]
rs1684421	0.88[JPT][hapmap]
rs1719830	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1719833	0.81[YRI][hapmap]
rs1719846	0.86[JPT][hapmap]
rs1719848	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1719852	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1719853	0.85[EUR][1000 genomes]
rs1719854	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1719855	0.81[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1719856	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1719858	0.86[EUR][1000 genomes]
rs1843640	0.91[JPT][hapmap]
rs1906043	0.91[JPT][hapmap]
rs2069211	0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs2101370	0.91[JPT][hapmap]
rs2388058	0.91[JPT][hapmap]
rs2730891	0.91[JPT][hapmap]
rs2730911	0.91[JPT][hapmap]
rs4293160	0.91[JPT][hapmap]
rs4768328	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4768330	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5005131	0.90[JPT][hapmap]
rs6580726	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7136593	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7957523	0.91[JPT][hapmap]
rs7976054	0.91[JPT][hapmap]
rs826838	0.85[CEU][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs826851	0.81[CEU][hapmap];0.80[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs826855	0.82[EUR][1000 genomes]
rs826856	0.87[EUR][1000 genomes]
rs826858	0.84[EUR][1000 genomes]
rs826861	0.85[YRI][hapmap]
rs826862	0.85[YRI][hapmap]
rs826870	0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs826873	0.87[EUR][1000 genomes]
rs826874	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs826876	0.80[CEU][hapmap]
rs826878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs826879	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs826886	0.85[CEU][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs826887	0.85[YRI][hapmap]
rs826888	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs826889	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs826891	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs826892	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs851934	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs860400	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs862331	0.81[YRI][hapmap]
rs864324	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs864325	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9645814	0.91[JPT][hapmap]
rs980571	0.80[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs980572	0.80[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs980573	0.84[EUR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs826893	ALG10B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39055800-39100800	Weak transcription	NHEK	skin
2	chr12:39056000-39114800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:39056000-39168600	Weak transcription	Hela-S3	cervix
4	chr12:39066200-39114400	Weak transcription	Pancreas	Pancrea
5	chr12:39069400-39114600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr12:39079200-39114400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:39080600-39115600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:39080800-39105000	Weak transcription	Adipose Nuclei	Adipose
9	chr12:39083400-39113200	Weak transcription	Left Ventricle	heart
10	chr12:39084200-39104800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:39086000-39114400	Weak transcription	Aorta	Aorta
12	chr12:39087200-39113800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr12:39089200-39113800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:39092600-39153600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:39094000-39103800	Weak transcription	GM12878-XiMat	blood
16	chr12:39094600-39114600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:39095000-39114000	Weak transcription	Liver	Liver
18	chr12:39095200-39114000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:39095800-39114600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:39095800-39117800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr12:39096800-39113800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr12:39098200-39101400	Weak transcription	Fetal Brain Male	brain
23	chr12:39099600-39100600	Weak transcription	Monocytes-CD14+_RO01746	blood

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