Variant report

Variant	rs844115
Chromosome Location	chr12:39117384-39117385
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10875979	0.84[EUR][1000 genomes]
rs10875991	0.84[EUR][1000 genomes]
rs1095575	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168985	0.81[EUR][1000 genomes]
rs11169031	0.81[EUR][1000 genomes]
rs11169142	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169144	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169169	0.84[EUR][1000 genomes]
rs11169301	0.85[EUR][1000 genomes]
rs11169387	0.81[EUR][1000 genomes]
rs12322306	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352122	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1352123	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403523	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1486345	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1486357	0.83[EUR][1000 genomes]
rs1684395	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1684406	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1684407	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1684411	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1684413	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1684414	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1684415	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1684416	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1719830	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1719848	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1719852	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1719853	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1719854	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1719855	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1719856	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1719858	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069211	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34254519	0.81[EUR][1000 genomes]
rs4768328	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768330	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55828987	0.81[EUR][1000 genomes]
rs6580726	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7136593	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826838	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826851	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826855	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs826856	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826858	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826870	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826873	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826874	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs826879	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826886	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs826888	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826889	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826891	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs826892	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs851934	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs860400	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs864324	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs864325	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs980571	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs980572	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs980573	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[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
rs844115	ALG10B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 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	chr12:39095800-39117800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr12:39110800-39119800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:39111800-39119400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr12:39112400-39118400	Weak transcription	Fetal Intestine Small	intestine
7	chr12:39113800-39117600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:39113800-39118400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:39113800-39123800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr12:39114000-39118400	Strong transcription	Liver	Liver
11	chr12:39114200-39133600	Weak transcription	A549	lung
12	chr12:39114400-39124800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:39114600-39117600	Strong transcription	Adipose Nuclei	Adipose
14	chr12:39114800-39117600	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr12:39115600-39117400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr12:39115600-39117800	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr12:39115800-39117400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr12:39115800-39117600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:39115800-39121000	Weak transcription	Gastric	stomach
20	chr12:39115800-39121400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:39115800-39121400	Weak transcription	Right Ventricle	heart
22	chr12:39115800-39121400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:39115800-39122400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:39115800-39123400	Weak transcription	Spleen	Spleen
25	chr12:39115800-39124000	Weak transcription	Pancreas	Pancrea
26	chr12:39115800-39164400	Weak transcription	Lung	lung
27	chr12:39116000-39117600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:39116000-39117600	Weak transcription	Fetal Intestine Large	intestine
29	chr12:39116000-39120800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:39116000-39123800	Weak transcription	Ovary	ovary
31	chr12:39116000-39126400	Weak transcription	Left Ventricle	heart
32	chr12:39116000-39154800	Weak transcription	Aorta	Aorta
33	chr12:39116400-39118000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr12:39116400-39118200	Weak transcription	Esophagus	oesophagus
35	chr12:39116400-39124400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:39116600-39118200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr12:39116800-39117600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr12:39116800-39117800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:39117000-39117800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:39117000-39118600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr12:39117000-39122600	Weak transcription	GM12878-XiMat	blood
42	chr12:39117000-39143200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr12:39117200-39119800	Weak transcription	Rectal Mucosa Donor 29	rectum

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