Variant report

Variant	rs12484983
Chromosome Location	chr22:30398273-30398274
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	chr22:30392517..30394667-chr22:30396187..30399023,2	MCF-7	breast:

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1160671	0.89[EUR][1000 genomes]
rs12233358	0.89[EUR][1000 genomes]
rs12484010	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12484420	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12484547	0.89[EUR][1000 genomes]
rs13053389	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13053765	0.89[EUR][1000 genomes]
rs13055998	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13056990	0.89[EUR][1000 genomes]
rs13057204	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13057580	0.89[EUR][1000 genomes]
rs13057878	0.84[AFR][1000 genomes]
rs13058334	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1476514	0.81[CHB][hapmap];0.89[EUR][1000 genomes]
rs16988123	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16988129	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs16988145	1.00[AFR][1000 genomes];0.97[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[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs34955393	1.00[EUR][1000 genomes]
rs35067150	0.89[EUR][1000 genomes]
rs35361418	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35710453	0.89[EUR][1000 genomes]
rs36018230	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3788422	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4343558	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4820821	1.00[EUR][1000 genomes]
rs4820825	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820829	0.89[EUR][1000 genomes]
rs4823056	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4823057	1.00[EUR][1000 genomes]
rs4823058	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4823064	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4823067	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4823071	0.89[EUR][1000 genomes]
rs4823080	0.81[CHB][hapmap]
rs55686007	0.83[AMR][1000 genomes]
rs5752969	1.00[EUR][1000 genomes]
rs5752976	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5752997	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753002	0.81[CHB][hapmap];0.89[EUR][1000 genomes]
rs5753007	0.89[EUR][1000 genomes]
rs5753013	0.89[EUR][1000 genomes]
rs5753014	0.81[CHB][hapmap];0.89[EUR][1000 genomes]
rs5753015	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5753019	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs5753020	0.89[EUR][1000 genomes]
rs5753022	0.89[EUR][1000 genomes]
rs5753027	0.89[EUR][1000 genomes]
rs5763543	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763544	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763552	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763553	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763556	1.00[EUR][1000 genomes]
rs5763557	1.00[EUR][1000 genomes]
rs5763561	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763566	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5763569	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763575	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs5763585	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763601	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763602	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763604	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763606	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763609	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763629	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763637	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763648	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763662	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763681	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763687	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763695	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763701	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763734	0.81[CHB][hapmap];0.89[EUR][1000 genomes]
rs5763742	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5763746	0.81[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5763748	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5763750	0.89[EUR][1000 genomes]
rs5763758	0.85[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	0.80[AMR][1000 genomes];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]
rs5763872	0.81[CHB][hapmap]
rs5997542	1.00[EUR][1000 genomes]
rs6006278	1.00[EUR][1000 genomes]
rs6006393	0.81[CHB][hapmap]
rs6519799	0.86[AFR][1000 genomes]
rs71331220	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718773	0.81[CHB][hapmap]
rs7286304	0.89[EUR][1000 genomes]
rs7286681	0.81[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7292355	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs739616	0.89[EUR][1000 genomes]
rs757026	0.90[CHB][hapmap];0.89[EUR][1000 genomes]
rs766011	0.89[EUR][1000 genomes]
rs8138404	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8142101	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs916807	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975704	0.81[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][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
rs12484983	LGALS8	trans	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30350600-30402600	Weak transcription	Aorta	Aorta
2	chr22:30363400-30427800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr22:30367000-30426600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr22:30375200-30403200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr22:30377600-30402800	Weak transcription	Fetal Brain Male	brain
6	chr22:30378200-30398800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr22:30384200-30398400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr22:30384200-30403800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr22:30384400-30404000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr22:30385000-30404000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr22:30386200-30402600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr22:30388000-30398400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr22:30388600-30400800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr22:30389000-30398600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr22:30389200-30398400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr22:30389200-30402600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr22:30389200-30403000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr22:30389200-30404200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr22:30389200-30409200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr22:30389200-30411600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr22:30389200-30411800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr22:30389800-30400600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr22:30390200-30398800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr22:30390200-30398800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr22:30390200-30403200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr22:30390200-30434200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr22:30390800-30398400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr22:30390800-30403000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr22:30391200-30402800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr22:30391200-30411400	Weak transcription	Small Intestine	intestine
31	chr22:30391400-30398600	Weak transcription	Brain Angular Gyrus	brain
32	chr22:30391400-30398600	Weak transcription	Right Ventricle	heart
33	chr22:30391400-30398800	Weak transcription	Gastric	stomach
34	chr22:30391400-30399400	Weak transcription	Brain Substantia Nigra	brain
35	chr22:30391400-30400800	Weak transcription	HSMMtube	muscle
36	chr22:30391400-30402600	Weak transcription	Ovary	ovary
37	chr22:30391400-30403000	Weak transcription	Pancreas	Pancrea
38	chr22:30391400-30403200	Weak transcription	Psoas Muscle	Psoas
39	chr22:30391400-30403600	Weak transcription	Hela-S3	cervix
40	chr22:30391400-30409800	Weak transcription	Fetal Heart	heart
41	chr22:30391400-30411600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr22:30391400-30433000	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr22:30391600-30400200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr22:30391600-30400200	Weak transcription	NHLF	lung
45	chr22:30391600-30404000	Weak transcription	Stomach Mucosa	stomach
46	chr22:30391600-30409800	Weak transcription	K562	blood
47	chr22:30391600-30417800	Weak transcription	Right Atrium	heart
48	chr22:30392200-30403000	Weak transcription	HMEC	breast
49	chr22:30392400-30398800	Weak transcription	A549	lung
50	chr22:30392600-30425000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links