Variant report

Variant	rs5752976
Chromosome Location	chr22:30281962-30281963
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs12233358	0.89[EUR][1000 genomes]
rs12484010	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12484420	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12484983	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13053389	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13053765	0.89[EUR][1000 genomes]
rs13055998	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13057204	0.89[EUR][1000 genomes]
rs13058224	0.85[AMR][1000 genomes]
rs13058334	0.97[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1476514	0.89[EUR][1000 genomes]
rs16988080	0.86[AFR][1000 genomes]
rs16988123	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16988145	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2010916	0.85[EUR][1000 genomes]
rs2012308	0.89[EUR][1000 genomes]
rs34955393	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35361418	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35710453	0.89[EUR][1000 genomes]
rs36018230	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3788422	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4343558	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4820821	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4820825	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4823056	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4823057	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4823058	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4823064	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4823067	0.89[EUR][1000 genomes]
rs4823071	0.89[EUR][1000 genomes]
rs55686007	0.90[AMR][1000 genomes]
rs5752969	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5752997	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753002	0.89[EUR][1000 genomes]
rs5753007	0.89[EUR][1000 genomes]
rs5763543	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5763544	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5763552	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5763553	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5763556	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5763557	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5763561	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5763566	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763569	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763575	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs5763585	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763601	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763602	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763604	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763606	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763609	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763629	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763637	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763648	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763662	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763681	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763687	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763695	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763701	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763734	0.89[EUR][1000 genomes]
rs5763742	0.89[EUR][1000 genomes]
rs5763746	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5763748	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5763750	0.89[EUR][1000 genomes]
rs5763758	0.83[AMR][1000 genomes]
rs5763759	0.89[EUR][1000 genomes]
rs5763763	0.89[EUR][1000 genomes]
rs5763766	0.89[EUR][1000 genomes]
rs5763769	0.89[EUR][1000 genomes]
rs5763774	0.89[EUR][1000 genomes]
rs5997542	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6006278	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71331220	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7286304	0.89[EUR][1000 genomes]
rs7286681	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7292355	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs739616	0.89[EUR][1000 genomes]
rs757026	0.89[EUR][1000 genomes]
rs8138404	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8142101	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs916807	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	esv1829662	chr22:30171725-30304390	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv1829425	chr22:30184378-30297376	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1851082	chr22:30253256-30294744	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv1833221	chr22:30274129-30297376	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv829161	chr22:30276811-30298332	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv829162	chr22:30276811-30298761	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv11554	chr22:30280400-30298271	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5752976	LGALS8	trans	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30278800-30282200	Active TSS	GM12878-XiMat	blood
2	chr22:30279600-30282400	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr22:30280000-30283400	Weak transcription	Esophagus	oesophagus
4	chr22:30280000-30283400	Weak transcription	Pancreas	Pancrea
5	chr22:30280000-30286200	Weak transcription	Gastric	stomach
6	chr22:30280200-30282000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr22:30280200-30282200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr22:30280200-30282600	Enhancers	Colon Smooth Muscle	Colon
9	chr22:30280200-30282600	Enhancers	Fetal Brain Male	brain
10	chr22:30280200-30283800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr22:30280200-30283800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr22:30280200-30283800	Enhancers	Fetal Heart	heart
13	chr22:30280200-30283800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr22:30280200-30284000	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr22:30280200-30293600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr22:30280200-30303800	Weak transcription	Aorta	Aorta
17	chr22:30280400-30282000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
18	chr22:30280400-30282200	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr22:30280400-30282400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr22:30280400-30282400	Weak transcription	A549	lung
21	chr22:30280400-30282600	Enhancers	Brain Hippocampus Middle	brain
22	chr22:30280400-30282600	Enhancers	Small Intestine	intestine
23	chr22:30280400-30282800	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr22:30280400-30283200	Weak transcription	Brain Angular Gyrus	brain
25	chr22:30280400-30283400	Weak transcription	Fetal Kidney	kidney
26	chr22:30280400-30283800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr22:30280400-30283800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr22:30280400-30283800	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr22:30280400-30283800	Enhancers	Fetal Lung	lung
30	chr22:30280400-30284000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr22:30280400-30297400	Weak transcription	K562	blood
32	chr22:30280600-30282000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr22:30280600-30282000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr22:30280600-30282000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr22:30280600-30282200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr22:30280600-30282200	Flanking Active TSS	Fetal Brain Female	brain
37	chr22:30280600-30282200	Enhancers	Fetal Stomach	stomach
38	chr22:30280600-30282600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr22:30280600-30282600	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr22:30280600-30282600	Enhancers	Liver	Liver
41	chr22:30280600-30284000	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr22:30280800-30282000	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr22:30280800-30282000	Enhancers	Duodenum Mucosa	Duodenum
44	chr22:30280800-30282000	Enhancers	Right Ventricle	heart
45	chr22:30280800-30282600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr22:30280800-30282600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr22:30280800-30282600	Enhancers	HepG2	liver
48	chr22:30280800-30282800	Enhancers	Rectal Smooth Muscle	rectum
49	chr22:30280800-30283200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr22:30280800-30283600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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