Variant report

Variant	rs5763872
Chromosome Location	chr22:30587850-30587851
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30587684..30589661-chr22:30601335..30603101,2	MCF-7	breast:
2	chr22:30587225..30588741-chr22:30589978..30592265,2	K562	blood:
3	chr22:30583372..30585537-chr22:30587327..30589279,2	K562	blood:
4	chr22:30580792..30583176-chr22:30587270..30589662,2	K562	blood:
5	chr22:30584790..30588358-chr22:30588911..30595947,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225676	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1160671	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12233358	0.84[EUR][1000 genomes]
rs12483946	0.92[CHB][hapmap];0.83[EUR][1000 genomes]
rs12484547	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12484740	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs12484983	0.81[CHB][hapmap]
rs13053765	0.84[EUR][1000 genomes]
rs13054837	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13055998	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs13056332	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13056990	0.84[EUR][1000 genomes]
rs13057204	0.84[EUR][1000 genomes]
rs13057580	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13057878	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1476514	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[EUR][1000 genomes]
rs2012308	0.84[EUR][1000 genomes]
rs2106430	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2106722	0.83[ASN][1000 genomes]
rs2214047	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2412977	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2412979	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34391152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34420020	0.95[EUR][1000 genomes]
rs34474867	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34545612	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35067150	0.84[EUR][1000 genomes]
rs35539897	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35710453	0.84[EUR][1000 genomes]
rs36018230	0.84[EUR][1000 genomes]
rs3788422	1.00[CEU][hapmap]
rs4820829	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4823067	0.84[EUR][1000 genomes]
rs4823071	0.84[EUR][1000 genomes]
rs4823080	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4823081	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4823082	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5753002	1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[EUR][1000 genomes]
rs5753007	0.84[EUR][1000 genomes]
rs5753013	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753014	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753015	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753019	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753020	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753022	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753027	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5753028	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5753029	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5753030	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5753046	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5753048	0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5763681	1.00[CEU][hapmap]
rs5763695	1.00[CEU][hapmap]
rs5763701	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs5763734	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[EUR][1000 genomes]
rs5763742	0.84[EUR][1000 genomes]
rs5763746	1.00[CEU][hapmap];0.92[CHB][hapmap];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];0.81[ASN][1000 genomes]
rs5763801	0.84[EUR][1000 genomes]
rs5763805	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5763810	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5763825	0.84[ASN][1000 genomes]
rs5763852	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5763854	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5763861	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6006393	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6006399	0.95[ASN][1000 genomes]
rs718773	0.93[CHB][hapmap]
rs7286304	0.84[EUR][1000 genomes]
rs7286681	1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[EUR][1000 genomes]
rs7288576	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs739616	0.84[EUR][1000 genomes]
rs757026	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[EUR][1000 genomes]
rs766011	1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8142101	1.00[CEU][hapmap]
rs916807	1.00[CEU][hapmap]
rs975704	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][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	nsv588884	chr22:30494371-30590026	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5763872	LGALS8	trans	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30576200-30588000	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr22:30577600-30589600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr22:30577600-30591400	Enhancers	A549	lung
4	chr22:30579600-30591400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr22:30580000-30588200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr22:30580200-30591400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr22:30581000-30588200	Weak transcription	Dnd41	blood
8	chr22:30581200-30591400	Weak transcription	Gastric	stomach
9	chr22:30581400-30589600	Weak transcription	Pancreas	Pancrea
10	chr22:30582200-30591400	Enhancers	HepG2	liver
11	chr22:30582800-30591200	Weak transcription	Stomach Mucosa	stomach
12	chr22:30582800-30591400	Weak transcription	Fetal Intestine Large	intestine
13	chr22:30583600-30588400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr22:30583800-30592200	Weak transcription	Small Intestine	intestine
15	chr22:30584400-30588200	Weak transcription	Primary T cells from cord blood	blood
16	chr22:30584400-30588200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr22:30584400-30591400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr22:30584400-30592000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr22:30584600-30588000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr22:30584800-30588200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr22:30584800-30591800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr22:30585000-30588200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr22:30585000-30591800	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr22:30585200-30590000	Enhancers	HSMMtube	muscle
25	chr22:30585400-30588000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr22:30585400-30591400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr22:30585600-30590600	Enhancers	Primary hematopoietic stem cells	blood
28	chr22:30586200-30588800	Enhancers	HSMM	muscle
29	chr22:30586400-30588600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr22:30586400-30589000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr22:30586400-30589000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr22:30586400-30589400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr22:30586400-30591600	Enhancers	Primary B cells from cord blood	blood
34	chr22:30586600-30588200	Weak transcription	GM12878-XiMat	blood
35	chr22:30586600-30588400	Enhancers	Osteobl	bone
36	chr22:30586600-30590600	Weak transcription	Spleen	Spleen
37	chr22:30587000-30588000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr22:30587000-30588200	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr22:30587000-30588200	Enhancers	Fetal Intestine Small	intestine
40	chr22:30587000-30588400	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr22:30587200-30588200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr22:30587200-30588400	Weak transcription	Fetal Thymus	thymus
43	chr22:30587200-30588600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr22:30587200-30589800	Weak transcription	NHLF	lung
45	chr22:30587200-30591400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr22:30587200-30591400	Weak transcription	Fetal Kidney	kidney
47	chr22:30587400-30589000	Enhancers	H9 Cell Line	embryonic stem cell
48	chr22:30587400-30589000	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr22:30587400-30589400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr22:30587400-30589600	Weak transcription	Placenta	Placenta

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