Variant report

Variant	rs826856
Chromosome Location	chr12:39115434-39115435
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10875979	0.91[EUR][1000 genomes]
rs10875991	0.92[EUR][1000 genomes]
rs1095575	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168985	0.89[EUR][1000 genomes]
rs11169031	0.89[EUR][1000 genomes]
rs11169142	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169144	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169169	0.91[EUR][1000 genomes]
rs11169301	0.93[EUR][1000 genomes]
rs11169387	0.88[EUR][1000 genomes]
rs12322306	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352122	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1352123	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403523	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1486345	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1486357	0.90[EUR][1000 genomes]
rs1684395	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1684406	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1684407	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1684411	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1684413	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1684414	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1684415	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1684416	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1719830	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1719848	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1719852	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1719853	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1719854	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1719855	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1719856	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1719858	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069211	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34254519	0.88[EUR][1000 genomes]
rs4768328	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768330	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55828987	0.89[EUR][1000 genomes]
rs6580726	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6580755	0.85[EUR][1000 genomes]
rs7136593	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826838	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826851	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs826858	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826870	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826873	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826874	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs826878	0.85[EUR][1000 genomes]
rs826879	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826886	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs826888	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826889	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826891	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs826892	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs826893	0.87[EUR][1000 genomes]
rs844115	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851934	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs860400	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs864324	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs864325	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs980571	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs980572	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs980573	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs826856	ALG10B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39056000-39168600	Weak transcription	Hela-S3	cervix
2	chr12:39080600-39115600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr12:39092600-39153600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:39095800-39117800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr12:39109800-39116800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:39110800-39119800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:39111000-39115600	Weak transcription	GM12878-XiMat	blood
8	chr12:39111800-39119400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr12:39112400-39118400	Weak transcription	Fetal Intestine Small	intestine
10	chr12:39113000-39117200	Weak transcription	Colonic Mucosa	Colon
11	chr12:39113200-39116000	Strong transcription	Left Ventricle	heart
12	chr12:39113800-39117000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr12:39113800-39117600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:39113800-39118400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:39113800-39123800	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr12:39114000-39115600	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr12:39114000-39115800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:39114000-39115800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:39114000-39117200	Weak transcription	Fetal Stomach	stomach
20	chr12:39114000-39118400	Strong transcription	Liver	Liver
21	chr12:39114200-39115800	Strong transcription	Right Ventricle	heart
22	chr12:39114200-39133600	Weak transcription	A549	lung
23	chr12:39114400-39115600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:39114400-39115600	Strong transcription	Pancreas	Pancrea
25	chr12:39114400-39116000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:39114400-39116000	Strong transcription	Aorta	Aorta
27	chr12:39114400-39124800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:39114600-39115800	ZNF genes & repeats	Gastric	stomach
29	chr12:39114600-39116000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:39114600-39116000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:39114600-39116400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:39114600-39116400	Strong transcription	Esophagus	oesophagus
33	chr12:39114600-39116400	Strong transcription	Stomach Smooth Muscle	stomach
34	chr12:39114600-39116800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:39114600-39117000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:39114600-39117600	Strong transcription	Adipose Nuclei	Adipose
37	chr12:39114800-39115800	ZNF genes & repeats	Lung	lung
38	chr12:39114800-39115800	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr12:39114800-39116600	Strong transcription	Fetal Muscle Trunk	muscle
40	chr12:39114800-39117600	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr12:39115000-39115800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr12:39115200-39115800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr12:39115200-39117200	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr12:39115400-39115800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr12:39115400-39115800	Genic enhancers	Spleen	Spleen
46	chr12:39115400-39116000	Strong transcription	Fetal Intestine Large	intestine
47	chr12:39115400-39116000	Strong transcription	Ovary	ovary

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