Variant report

Variant	rs5753046
Chromosome Location	chr22:30602246-30602247
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30600518..30603071-chr22:30604454..30606610,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1160671	0.84[EUR][1000 genomes]
rs12233358	0.84[EUR][1000 genomes]
rs12483946	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12484547	0.84[EUR][1000 genomes]
rs12484740	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13053765	0.84[EUR][1000 genomes]
rs13054837	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13055998	0.84[EUR][1000 genomes]
rs13056332	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13056990	0.84[EUR][1000 genomes]
rs13057204	0.84[EUR][1000 genomes]
rs13057580	0.84[EUR][1000 genomes]
rs13057878	0.95[EUR][1000 genomes]
rs1476514	0.84[EUR][1000 genomes]
rs2012308	0.84[EUR][1000 genomes]
rs2106430	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214047	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2412977	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2412979	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34391152	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34420020	0.95[EUR][1000 genomes]
rs34474867	0.95[EUR][1000 genomes]
rs34545612	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35067150	0.84[EUR][1000 genomes]
rs35539897	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35710453	0.84[EUR][1000 genomes]
rs36018230	0.84[EUR][1000 genomes]
rs4820829	0.84[EUR][1000 genomes]
rs4823067	0.84[EUR][1000 genomes]
rs4823071	0.84[EUR][1000 genomes]
rs4823080	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4823081	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4823082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753002	0.84[EUR][1000 genomes]
rs5753007	0.84[EUR][1000 genomes]
rs5753013	0.84[EUR][1000 genomes]
rs5753014	0.84[EUR][1000 genomes]
rs5753015	0.84[EUR][1000 genomes]
rs5753019	0.84[EUR][1000 genomes]
rs5753020	0.84[EUR][1000 genomes]
rs5753022	0.84[EUR][1000 genomes]
rs5753027	0.84[EUR][1000 genomes]
rs5753028	0.95[EUR][1000 genomes]
rs5753029	0.95[EUR][1000 genomes]
rs5753030	0.95[EUR][1000 genomes]
rs5753048	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5763701	0.84[EUR][1000 genomes]
rs5763734	0.84[EUR][1000 genomes]
rs5763742	0.84[EUR][1000 genomes]
rs5763746	0.84[EUR][1000 genomes]
rs5763748	0.84[EUR][1000 genomes]
rs5763750	0.84[EUR][1000 genomes]
rs5763759	0.84[EUR][1000 genomes]
rs5763763	0.84[EUR][1000 genomes]
rs5763766	0.84[EUR][1000 genomes]
rs5763769	0.84[EUR][1000 genomes]
rs5763774	0.84[EUR][1000 genomes]
rs5763782	0.84[EUR][1000 genomes]
rs5763788	0.84[EUR][1000 genomes]
rs5763801	0.84[EUR][1000 genomes]
rs5763805	0.84[EUR][1000 genomes]
rs5763810	0.84[EUR][1000 genomes]
rs5763852	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5763854	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5763861	0.95[EUR][1000 genomes]
rs5763872	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6006393	0.95[ASN][1000 genomes]
rs6006399	1.00[ASN][1000 genomes]
rs7286304	0.84[EUR][1000 genomes]
rs7286681	0.84[EUR][1000 genomes]
rs7288576	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs739616	0.84[EUR][1000 genomes]
rs757026	0.84[EUR][1000 genomes]
rs766011	0.84[EUR][1000 genomes]
rs975704	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv834173	chr22:30515092-30658277	Enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv432239	chr22:30580161-30669883	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5753046	LGALS8	trans	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30592800-30602800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr22:30592800-30604800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr22:30593600-30603000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr22:30597600-30603000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr22:30597600-30609800	Enhancers	Stomach Mucosa	stomach
6	chr22:30597600-30610000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr22:30597800-30602400	Enhancers	Duodenum Mucosa	Duodenum
8	chr22:30598600-30607000	Enhancers	Placenta	Placenta
9	chr22:30599000-30602800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr22:30599000-30605200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr22:30599200-30602800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr22:30599800-30602800	Weak transcription	Lung	lung
13	chr22:30599800-30605600	Enhancers	NHLF	lung
14	chr22:30600000-30603600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr22:30600000-30604200	Weak transcription	Fetal Kidney	kidney
16	chr22:30600000-30605000	Weak transcription	Pancreas	Pancrea
17	chr22:30600200-30607800	Enhancers	NH-A	brain
18	chr22:30600400-30606000	Enhancers	Ovary	ovary
19	chr22:30600400-30607000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr22:30600400-30607000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr22:30600400-30607200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr22:30600400-30610000	Enhancers	HMEC	breast
23	chr22:30600600-30603800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr22:30600600-30605000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr22:30600800-30606200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr22:30601000-30610000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr22:30601200-30602400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr22:30601200-30603200	Bivalent Enhancer	Fetal Muscle Leg	muscle
29	chr22:30601200-30603600	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr22:30601400-30603000	Weak transcription	Gastric	stomach
31	chr22:30601400-30603200	Enhancers	Brain Angular Gyrus	brain
32	chr22:30601400-30605600	Enhancers	HUVEC	blood vessel
33	chr22:30601400-30606600	Enhancers	HepG2	liver
34	chr22:30601600-30602400	Enhancers	Brain Substantia Nigra	brain
35	chr22:30601600-30602600	Enhancers	Primary B cells from cord blood	blood
36	chr22:30601600-30602600	Enhancers	HSMMtube	muscle
37	chr22:30601600-30603200	Enhancers	Fetal Intestine Large	intestine
38	chr22:30601600-30604200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr22:30601600-30605600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr22:30601600-30605800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr22:30601600-30606600	Enhancers	Hela-S3	cervix
42	chr22:30601800-30602400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr22:30601800-30602800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr22:30601800-30603800	Enhancers	NHEK	skin
45	chr22:30601800-30604200	Weak transcription	Colonic Mucosa	Colon
46	chr22:30601800-30604400	Weak transcription	Fetal Thymus	thymus
47	chr22:30601800-30604600	Enhancers	NHDF-Ad	bronchial
48	chr22:30601800-30605400	Weak transcription	Esophagus	oesophagus
49	chr22:30601800-30609800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr22:30601800-30610400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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