Variant report

Variant	rs4823064
Chromosome Location	chr22:30309155-30309156
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30303958..30305806-chr22:30307869..30310153,2	K562	blood:
2	chr22:30303040..30305497-chr22:30307951..30311073,3	MCF-7	breast:
3	chr22:30308576..30310461-chr22:30376998..30379736,2	K562	blood:
4	chr22:30277897..30280164-chr22:30306298..30309228,2	K562	blood:

Variant related genes	Relation type
ENSG00000100330	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs12233358	0.89[EUR][1000 genomes]
rs12484010	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12484420	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12484547	0.89[EUR][1000 genomes]
rs12484983	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13053389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13053765	0.89[EUR][1000 genomes]
rs13055998	0.84[AFR][1000 genomes];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]
rs13058224	0.85[AMR][1000 genomes]
rs13058334	0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1476514	0.89[EUR][1000 genomes]
rs16988080	0.81[AFR][1000 genomes]
rs16988123	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16988129	0.81[AFR][1000 genomes]
rs16988145	0.95[AFR][1000 genomes];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]
rs34955393	1.00[EUR][1000 genomes]
rs35067150	0.89[EUR][1000 genomes]
rs35361418	1.00[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	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3788422	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4343558	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4820821	1.00[EUR][1000 genomes]
rs4820825	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820829	0.89[EUR][1000 genomes]
rs4823056	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4823057	1.00[EUR][1000 genomes]
rs4823058	0.88[AMR][1000 genomes];1.00[EUR][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]
rs5752976	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5752997	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753002	0.89[EUR][1000 genomes]
rs5753007	0.89[EUR][1000 genomes]
rs5753013	0.89[EUR][1000 genomes]
rs5753014	0.89[EUR][1000 genomes]
rs5753015	0.89[EUR][1000 genomes]
rs5753019	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs5753020	0.89[EUR][1000 genomes]
rs5753022	0.89[EUR][1000 genomes]
rs5763543	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763544	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763552	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763553	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763556	1.00[EUR][1000 genomes]
rs5763557	1.00[EUR][1000 genomes]
rs5763561	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763566	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5763569	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763575	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs5763585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763601	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763602	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763604	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763606	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763609	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763629	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763637	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763648	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763662	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763681	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763687	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763695	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763701	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763734	0.89[EUR][1000 genomes]
rs5763742	0.89[EUR][1000 genomes]
rs5763746	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5763748	0.89[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]
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]
rs5997542	1.00[EUR][1000 genomes]
rs6006278	1.00[EUR][1000 genomes]
rs6519799	0.81[AFR][1000 genomes]
rs71331220	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7286304	0.89[EUR][1000 genomes]
rs7286681	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7292355	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs739616	0.89[EUR][1000 genomes]
rs757026	0.89[EUR][1000 genomes]
rs766011	0.89[EUR][1000 genomes]
rs8138404	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8142101	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs916807	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4823064	LGALS8	trans	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30281400-30312200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr22:30282200-30310200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr22:30287000-30319600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr22:30290400-30312000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr22:30298000-30314600	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr22:30304000-30309800	Weak transcription	Brain Germinal Matrix	brain
7	chr22:30304200-30312800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr22:30304400-30309200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr22:30304400-30310800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr22:30304400-30312000	Weak transcription	Fetal Kidney	kidney
11	chr22:30304400-30312400	Weak transcription	Brain Hippocampus Middle	brain
12	chr22:30304400-30321000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr22:30304600-30309200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr22:30304600-30309400	Weak transcription	Brain Anterior Caudate	brain
15	chr22:30304600-30310000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr22:30304600-30310000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr22:30304600-30312200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr22:30304800-30312400	Weak transcription	Brain Substantia Nigra	brain
19	chr22:30305200-30310400	Weak transcription	Primary B cells from cord blood	blood
20	chr22:30305200-30310600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr22:30305400-30310000	Weak transcription	Hela-S3	cervix
22	chr22:30305400-30310400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr22:30305600-30327400	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr22:30305800-30310400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr22:30306600-30312200	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr22:30306800-30310000	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr22:30306800-30310200	Enhancers	Psoas Muscle	Psoas
28	chr22:30307000-30310000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr22:30307000-30314800	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr22:30307200-30309200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr22:30307200-30309200	Enhancers	Stomach Mucosa	stomach
32	chr22:30307200-30309200	Enhancers	HepG2	liver
33	chr22:30307200-30310000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr22:30307400-30310000	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr22:30307400-30310400	Enhancers	Fetal Heart	heart
36	chr22:30307400-30321000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr22:30307400-30321200	Weak transcription	Esophagus	oesophagus
38	chr22:30307800-30309400	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr22:30307800-30309400	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr22:30307800-30310000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr22:30307800-30311400	Enhancers	A549	lung
42	chr22:30307800-30314200	Enhancers	Colon Smooth Muscle	Colon
43	chr22:30308000-30309200	Enhancers	Fetal Intestine Small	intestine
44	chr22:30308000-30309200	Enhancers	Pancreas	Pancrea
45	chr22:30308000-30309400	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr22:30308000-30309400	Enhancers	Ovary	ovary
47	chr22:30308000-30309800	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr22:30308000-30310000	Enhancers	Left Ventricle	heart
49	chr22:30308000-30310200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr22:30308000-30310400	Enhancers	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links