Variant report

Variant	rs5763662
Chromosome Location	chr22:30378703-30378704
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30308576..30310461-chr22:30376998..30379736,2	K562	blood:
2	chr22:30376984..30378787-chr22:30386876..30389530,2	MCF-7	breast:

Extended variants
information (count: 107 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1160671	0.89[EUR][1000 genomes]
rs12233358	0.89[EUR][1000 genomes]
rs12484010	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12484420	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12484547	0.89[EUR][1000 genomes]
rs12484983	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13053389	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13053765	0.89[EUR][1000 genomes]
rs13055998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13056990	0.89[EUR][1000 genomes]
rs13057204	0.89[EUR][1000 genomes]
rs13057580	0.89[EUR][1000 genomes]
rs13058334	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1476514	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs16988123	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16988145	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010916	0.85[EUR][1000 genomes]
rs2012308	0.89[EUR][1000 genomes]
rs2412961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34955393	1.00[EUR][1000 genomes]
rs35067150	0.89[EUR][1000 genomes]
rs35361418	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35710453	0.89[EUR][1000 genomes]
rs36018230	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3788422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4343558	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4820821	1.00[EUR][1000 genomes]
rs4820825	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820829	0.89[EUR][1000 genomes]
rs4823056	1.00[EUR][1000 genomes]
rs4823057	1.00[EUR][1000 genomes]
rs4823058	1.00[EUR][1000 genomes]
rs4823064	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4823067	0.89[EUR][1000 genomes]
rs4823071	0.89[EUR][1000 genomes]
rs55686007	0.80[AMR][1000 genomes]
rs5752969	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5752976	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5752997	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753002	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[EUR][1000 genomes]
rs5753007	0.89[EUR][1000 genomes]
rs5753013	0.89[EUR][1000 genomes]
rs5753014	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[EUR][1000 genomes]
rs5753015	0.89[EUR][1000 genomes]
rs5753019	0.89[EUR][1000 genomes]
rs5753020	0.89[EUR][1000 genomes]
rs5753022	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5753027	0.89[EUR][1000 genomes]
rs5753030	1.00[AFR][1000 genomes]
rs5763543	1.00[EUR][1000 genomes]
rs5763544	1.00[EUR][1000 genomes]
rs5763552	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763553	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763556	1.00[EUR][1000 genomes]
rs5763557	1.00[EUR][1000 genomes]
rs5763561	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763566	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5763569	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763575	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs5763585	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763601	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763602	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763604	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763606	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763609	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763629	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763637	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763648	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763687	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763734	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs5763742	0.89[EUR][1000 genomes]
rs5763746	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5763748	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5763750	0.89[EUR][1000 genomes]
rs5763758	1.00[AFR][1000 genomes];0.92[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]
rs5763782	0.89[EUR][1000 genomes]
rs5763788	0.89[EUR][1000 genomes]
rs5763801	0.89[EUR][1000 genomes]
rs5763805	0.89[EUR][1000 genomes]
rs5763810	0.89[EUR][1000 genomes]
rs5763861	1.00[AFR][1000 genomes]
rs5997542	1.00[EUR][1000 genomes]
rs6006278	1.00[EUR][1000 genomes]
rs71331220	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718773	0.84[CHB][hapmap]
rs7286304	0.89[EUR][1000 genomes]
rs7286681	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7292355	1.00[EUR][1000 genomes]
rs739616	0.89[EUR][1000 genomes]
rs757026	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[EUR][1000 genomes]
rs766011	0.89[EUR][1000 genomes]
rs8138404	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8142101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs916807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975704	1.00[CEU][hapmap];0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv523696	chr22:30326102-30381789	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv3591	chr22:30344208-30388897	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
LDL cholesterol	24097068	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5763662	LGALS8	trans	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30345400-30379000	Weak transcription	Esophagus	oesophagus
2	chr22:30348400-30387200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr22:30350600-30402600	Weak transcription	Aorta	Aorta
4	chr22:30351200-30385800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr22:30351200-30387400	Weak transcription	Ovary	ovary
6	chr22:30352800-30388600	Weak transcription	HepG2	liver
7	chr22:30354600-30390200	Weak transcription	Colonic Mucosa	Colon
8	chr22:30354800-30390400	Weak transcription	Small Intestine	intestine
9	chr22:30358800-30387400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr22:30363400-30427800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr22:30366000-30384200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr22:30366400-30387400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr22:30366600-30390800	Weak transcription	Gastric	stomach
14	chr22:30367000-30426600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr22:30367400-30397800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr22:30368400-30382800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr22:30368400-30387400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr22:30369400-30382600	Weak transcription	Brain Anterior Caudate	brain
19	chr22:30369400-30388400	Weak transcription	NH-A	brain
20	chr22:30370000-30391000	Weak transcription	Fetal Heart	heart
21	chr22:30370200-30388400	Weak transcription	NHLF	lung
22	chr22:30370600-30390800	Weak transcription	Right Ventricle	heart
23	chr22:30370800-30379400	Weak transcription	HSMM	muscle
24	chr22:30370800-30387400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr22:30370800-30390000	Weak transcription	Stomach Mucosa	stomach
26	chr22:30371000-30383200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr22:30371200-30382000	Weak transcription	Brain Substantia Nigra	brain
28	chr22:30371800-30385800	Weak transcription	Lung	lung
29	chr22:30371800-30386600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr22:30373400-30383000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr22:30373400-30388600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr22:30373600-30383400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr22:30373600-30383600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr22:30373600-30388600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr22:30373800-30391400	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr22:30374000-30380000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr22:30374200-30389600	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr22:30374400-30383400	Weak transcription	Brain Hippocampus Middle	brain
39	chr22:30374400-30383600	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr22:30374600-30381800	Strong transcription	Primary B cells from cord blood	blood
41	chr22:30374800-30380800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr22:30375200-30386000	Weak transcription	Thymus	Thymus
43	chr22:30375200-30389800	Weak transcription	K562	blood
44	chr22:30375200-30403200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr22:30375400-30381200	Strong transcription	Primary T cells from cord blood	blood
46	chr22:30375400-30390800	Weak transcription	Pancreas	Pancrea
47	chr22:30375800-30381600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr22:30375800-30387400	Weak transcription	Spleen	Spleen
49	chr22:30375800-30388400	Weak transcription	A549	lung
50	chr22:30375800-30389800	Weak transcription	HUVEC	blood vessel

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