Variant report

Variant	rs2010916
Chromosome Location	chr22:30441219-30441220
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30431981..30436228-chr22:30436988..30442132,5	MCF-7	breast:
2	chr22:30438959..30441360-chr22:30444490..30446436,2	K562	blood:

Extended variants
information (count: 117 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1122239	0.98[ASN][1000 genomes]
rs1160671	0.95[EUR][1000 genomes]
rs12233358	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12484010	0.85[EUR][1000 genomes]
rs12484420	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12484547	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12484983	0.85[EUR][1000 genomes]
rs13053389	0.85[EUR][1000 genomes]
rs13053765	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13054837	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13055998	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13056332	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13056990	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13057204	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13057580	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13057733	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13057878	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1476514	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16988123	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16988145	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2012308	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2214047	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2412977	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2412979	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34420020	0.85[EUR][1000 genomes]
rs34474867	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34545612	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34955393	0.85[EUR][1000 genomes]
rs35067150	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35710453	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36018230	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3788422	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4343558	0.85[EUR][1000 genomes]
rs4820821	0.85[EUR][1000 genomes]
rs4820825	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4820829	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4823056	0.85[EUR][1000 genomes]
rs4823057	0.85[EUR][1000 genomes]
rs4823058	0.85[EUR][1000 genomes]
rs4823064	0.85[EUR][1000 genomes]
rs4823067	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4823071	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5752969	0.85[EUR][1000 genomes]
rs5752976	0.85[EUR][1000 genomes]
rs5752997	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5753002	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5753007	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5753013	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753014	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753015	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753019	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753020	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753022	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753027	0.95[EUR][1000 genomes]
rs5753028	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753029	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753030	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5763543	0.85[EUR][1000 genomes]
rs5763544	0.85[EUR][1000 genomes]
rs5763552	0.85[EUR][1000 genomes]
rs5763553	0.85[EUR][1000 genomes]
rs5763556	0.85[EUR][1000 genomes]
rs5763557	0.85[EUR][1000 genomes]
rs5763561	0.85[EUR][1000 genomes]
rs5763566	0.85[EUR][1000 genomes]
rs5763569	0.85[EUR][1000 genomes]
rs5763585	0.85[EUR][1000 genomes]
rs5763601	0.85[EUR][1000 genomes]
rs5763602	0.85[EUR][1000 genomes]
rs5763604	0.85[EUR][1000 genomes]
rs5763606	0.85[EUR][1000 genomes]
rs5763609	0.85[EUR][1000 genomes]
rs5763629	0.85[EUR][1000 genomes]
rs5763637	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5763648	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5763662	0.85[EUR][1000 genomes]
rs5763681	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5763687	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5763695	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5763701	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5763734	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763742	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5763746	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5763748	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5763749	0.90[ASN][1000 genomes]
rs5763750	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5763758	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5763759	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5763763	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5763766	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5763769	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5763774	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5763782	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5763788	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5763801	0.95[EUR][1000 genomes]
rs5763805	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5763810	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5763852	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5763854	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5763861	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5997542	0.85[EUR][1000 genomes]
rs6006278	0.85[EUR][1000 genomes]
rs71331220	0.85[EUR][1000 genomes]
rs718773	0.84[ASN][1000 genomes]
rs7286304	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7286681	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7292355	0.85[EUR][1000 genomes]
rs739616	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs757026	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs766011	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8138404	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8142101	0.85[EUR][1000 genomes]
rs916807	0.82[AMR][1000 genomes]
rs975704	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv964619	chr22:30440663-30444496	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2010916	LGALS8	trans	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30423600-30447600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr22:30424800-30443000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr22:30425800-30442000	Weak transcription	Fetal Brain Female	brain
4	chr22:30426600-30443000	Weak transcription	Thymus	Thymus
5	chr22:30430200-30442800	Weak transcription	Spleen	Spleen
6	chr22:30430200-30449600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr22:30435000-30450600	Weak transcription	Gastric	stomach
8	chr22:30437000-30443400	Weak transcription	Esophagus	oesophagus
9	chr22:30438200-30448200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr22:30438800-30441800	Enhancers	Fetal Intestine Large	intestine
11	chr22:30439200-30441400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr22:30439200-30441400	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr22:30439400-30441600	Enhancers	Duodenum Mucosa	Duodenum
14	chr22:30439400-30441800	Enhancers	Fetal Intestine Small	intestine
15	chr22:30439600-30441400	Enhancers	Adipose Nuclei	Adipose
16	chr22:30439600-30442200	Enhancers	Stomach Mucosa	stomach
17	chr22:30439800-30441600	Enhancers	Pancreas	Pancrea
18	chr22:30440400-30441600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr22:30440600-30441400	Enhancers	Lung	lung
20	chr22:30440600-30441400	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr22:30440600-30442800	Weak transcription	HepG2	liver
22	chr22:30440800-30441400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr22:30440800-30441800	Enhancers	Fetal Stomach	stomach
24	chr22:30440800-30441800	Enhancers	Hela-S3	cervix
25	chr22:30440800-30444400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr22:30441000-30441400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr22:30441000-30444400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr22:30441200-30441600	Enhancers	Fetal Muscle Leg	muscle
29	chr22:30441200-30442000	Enhancers	Fetal Muscle Trunk	muscle
30	chr22:30441200-30443000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr22:30441200-30443400	Weak transcription	Liver	Liver
32	chr22:30441200-30444600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links