Variant report

Variant	rs12233358
Chromosome Location	chr22:30432631-30432632
allele	C/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	chr22:30422072..30424953-chr22:30431511..30433741,2	MCF-7	breast:

Extended variants
information (count: 133 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1122239	0.92[ASN][1000 genomes]
rs1160671	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12483946	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs12484010	0.89[EUR][1000 genomes]
rs12484420	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12484547	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12484740	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs12484983	0.81[CHB][hapmap];0.89[EUR][1000 genomes]
rs12537	0.82[CHD][hapmap]
rs13053389	0.89[EUR][1000 genomes]
rs13053765	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13054837	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13055998	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13056332	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13056990	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13057204	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13057580	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13057733	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13057878	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1476514	0.91[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16988123	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16988145	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2010916	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2012308	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2106430	0.84[EUR][1000 genomes]
rs2106722	0.80[ASN][1000 genomes]
rs2214047	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2412961	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2412977	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2412979	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34391152	0.84[EUR][1000 genomes]
rs34420020	0.89[EUR][1000 genomes]
rs34474867	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34545612	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34955393	0.89[EUR][1000 genomes]
rs35067150	1.00[EUR][1000 genomes]
rs35361418	0.84[EUR][1000 genomes]
rs35539897	0.84[EUR][1000 genomes]
rs35710453	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36018230	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3788422	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4343558	0.89[EUR][1000 genomes]
rs4820821	0.89[EUR][1000 genomes]
rs4820825	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4820829	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4823056	0.89[EUR][1000 genomes]
rs4823057	0.89[EUR][1000 genomes]
rs4823058	0.89[EUR][1000 genomes]
rs4823064	0.89[EUR][1000 genomes]
rs4823067	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4823071	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4823080	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs4823082	0.84[EUR][1000 genomes]
rs5752969	0.89[EUR][1000 genomes]
rs5752976	0.89[EUR][1000 genomes]
rs5752997	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5753002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753007	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5753013	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5753014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5753015	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5753019	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5753020	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5753022	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5753027	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5753028	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5753029	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5753030	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5753046	0.84[EUR][1000 genomes]
rs5753048	1.00[CEU][hapmap]
rs5763543	0.89[EUR][1000 genomes]
rs5763544	0.89[EUR][1000 genomes]
rs5763552	0.89[EUR][1000 genomes]
rs5763553	0.89[EUR][1000 genomes]
rs5763556	0.89[EUR][1000 genomes]
rs5763557	0.89[EUR][1000 genomes]
rs5763561	0.89[EUR][1000 genomes]
rs5763566	0.89[EUR][1000 genomes]
rs5763569	0.89[EUR][1000 genomes]
rs5763585	0.89[EUR][1000 genomes]
rs5763601	0.89[EUR][1000 genomes]
rs5763602	0.89[EUR][1000 genomes]
rs5763604	0.89[EUR][1000 genomes]
rs5763606	0.89[EUR][1000 genomes]
rs5763609	0.89[EUR][1000 genomes]
rs5763629	0.89[EUR][1000 genomes]
rs5763637	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5763648	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5763662	0.89[EUR][1000 genomes]
rs5763681	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5763687	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5763695	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5763701	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763734	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763742	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763748	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763749	1.00[ASN][1000 genomes]
rs5763750	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5763758	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5763759	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5763763	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5763766	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5763769	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5763774	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5763782	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5763787	0.82[ASN][1000 genomes]
rs5763788	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763801	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5763805	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763810	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763825	0.82[ASN][1000 genomes]
rs5763852	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763854	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763861	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763872	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[EUR][1000 genomes]
rs5997542	0.89[EUR][1000 genomes]
rs6006278	0.89[EUR][1000 genomes]
rs6006393	0.92[CHB][hapmap];0.82[GIH][hapmap]
rs71331220	0.89[EUR][1000 genomes]
rs718773	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7286304	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7286681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7292355	0.89[EUR][1000 genomes]
rs739616	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs757026	0.91[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs766011	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8138404	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8142101	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[EUR][1000 genomes]
rs916807	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs975704	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.85[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
rs12233358	LGALS8	trans	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30390200-30434200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:30391400-30433000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr22:30409000-30432800	Strong transcription	Fetal Stomach	stomach
4	chr22:30419600-30434400	Weak transcription	Small Intestine	intestine
5	chr22:30422400-30434200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr22:30422400-30434200	Weak transcription	HUVEC	blood vessel
7	chr22:30423400-30434400	Weak transcription	A549	lung
8	chr22:30423600-30447600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr22:30424200-30434000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr22:30424600-30435600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr22:30424800-30443000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr22:30425000-30434200	Weak transcription	Gastric	stomach
13	chr22:30425200-30434000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr22:30425200-30434200	Weak transcription	Pancreas	Pancrea
15	chr22:30425200-30434200	Weak transcription	NHLF	lung
16	chr22:30425200-30435800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr22:30425200-30438800	Weak transcription	Fetal Intestine Large	intestine
18	chr22:30425200-30440000	Weak transcription	Fetal Lung	lung
19	chr22:30425200-30440200	Weak transcription	Brain Germinal Matrix	brain
20	chr22:30425600-30439400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr22:30425800-30433000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr22:30425800-30433800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr22:30425800-30434000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr22:30425800-30434800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr22:30425800-30435400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr22:30425800-30439800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr22:30425800-30442000	Weak transcription	Fetal Brain Female	brain
28	chr22:30426000-30434400	Weak transcription	Left Ventricle	heart
29	chr22:30426200-30434000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr22:30426200-30434200	Weak transcription	Lung	lung
31	chr22:30426600-30443000	Weak transcription	Thymus	Thymus
32	chr22:30429200-30434200	Weak transcription	Psoas Muscle	Psoas
33	chr22:30429400-30439800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr22:30429800-30433000	Weak transcription	Ovary	ovary
35	chr22:30429800-30434600	Weak transcription	Right Atrium	heart
36	chr22:30429800-30435000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr22:30430200-30432800	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr22:30430200-30434000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr22:30430200-30434000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr22:30430200-30442800	Weak transcription	Spleen	Spleen
41	chr22:30430200-30449600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr22:30430400-30433600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr22:30430400-30434400	Weak transcription	Liver	Liver
44	chr22:30430400-30434400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr22:30430400-30435800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr22:30430800-30436200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr22:30430800-30439400	Weak transcription	Fetal Intestine Small	intestine
48	chr22:30431200-30432800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr22:30431400-30432800	Enhancers	Adipose Nuclei	Adipose
50	chr22:30431400-30432800	Enhancers	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links