Variant report

Variant	rs2046498
Chromosome Location	chr12:51365312-51365313
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	chr12:51363073..51365710-chr12:51419692..51421851,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110911	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10876126	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1095997	0.85[AMR][1000 genomes]
rs1095998	0.84[EUR][1000 genomes]
rs11169679	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12423207	0.82[CEU][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs150909	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs161044	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs161045	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs161046	0.82[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs161047	0.82[CEU][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17125370	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs17229232	1.00[GIH][hapmap];0.85[TSI][hapmap]
rs224564	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs224566	0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs224569	0.82[CEU][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs224570	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs224573	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs224574	0.82[CEU][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs224578	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs224585	0.88[EUR][1000 genomes]
rs224586	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs224590	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs224592	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs224593	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2554858	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2554859	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2554861	0.92[EUR][1000 genomes]
rs2630353	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2630358	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630362	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2630366	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2630367	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs319930	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs319938	1.00[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs319940	0.88[EUR][1000 genomes]
rs319941	0.86[EUR][1000 genomes]
rs319943	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs319944	0.92[EUR][1000 genomes]
rs364627	0.82[CEU][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs390424	0.82[CEU][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs394384	0.82[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs416062	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4238110	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs435965	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs445520	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs452587	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4768875	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4768959	1.00[MEX][hapmap];0.80[YRI][hapmap]
rs55874852	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs613977	0.84[EUR][1000 genomes]
rs618510	0.83[AMR][1000 genomes]
rs6580779	0.82[CEU][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6580780	0.82[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs686528	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs706803	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706804	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138860	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7299484	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7969536	0.81[AMR][1000 genomes]
rs7971712	1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs7972608	1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap]
rs7974923	1.00[MEX][hapmap];0.80[YRI][hapmap]
rs7975628	1.00[MEX][hapmap];0.80[YRI][hapmap]
rs7978782	0.80[YRI][hapmap]
rs829016	0.92[EUR][1000 genomes]
rs829021	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853236	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1053466	chr12:51350285-51375969	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2046498	SLC11A2	cis	lymphoblastoid	seeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51323000-51377200	Weak transcription	Aorta	Aorta
2	chr12:51328800-51378000	Weak transcription	Brain Substantia Nigra	brain
3	chr12:51329600-51373600	Weak transcription	Left Ventricle	heart
4	chr12:51331400-51378400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:51331600-51373800	Weak transcription	Pancreas	Pancrea
6	chr12:51331800-51382000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:51331800-51382000	Weak transcription	Ovary	ovary
8	chr12:51341600-51378200	Weak transcription	Right Ventricle	heart
9	chr12:51341800-51372600	Weak transcription	Osteobl	bone
10	chr12:51341800-51383200	Weak transcription	Fetal Brain Male	brain
11	chr12:51342400-51373200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:51342800-51378400	Weak transcription	NHLF	lung
13	chr12:51343000-51366200	Weak transcription	Brain Germinal Matrix	brain
14	chr12:51343600-51366200	Weak transcription	Gastric	stomach
15	chr12:51344000-51382000	Weak transcription	Esophagus	oesophagus
16	chr12:51344600-51381600	Weak transcription	Spleen	Spleen
17	chr12:51347200-51378000	Weak transcription	Brain Angular Gyrus	brain
18	chr12:51347400-51378000	Weak transcription	Brain Anterior Caudate	brain
19	chr12:51350800-51380600	Weak transcription	Fetal Lung	lung
20	chr12:51354400-51383800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr12:51355600-51378000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr12:51355800-51366200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:51355800-51378000	Weak transcription	A549	lung
24	chr12:51356000-51372600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr12:51357600-51378000	Weak transcription	Psoas Muscle	Psoas
26	chr12:51358200-51366200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:51358800-51377800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr12:51359800-51380400	Weak transcription	Fetal Kidney	kidney
29	chr12:51360000-51366400	Strong transcription	Fetal Thymus	thymus
30	chr12:51360200-51365600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:51360200-51374400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr12:51360200-51381800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:51360400-51365800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr12:51360400-51372600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:51360400-51374400	Weak transcription	HUVEC	blood vessel
36	chr12:51360600-51381000	Weak transcription	Primary B cells from cord blood	blood
37	chr12:51360600-51381800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:51361600-51365400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:51361600-51382200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr12:51361800-51365800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr12:51362000-51366200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr12:51362000-51366200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:51362200-51365600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:51362200-51372600	Weak transcription	Adipose Nuclei	Adipose
45	chr12:51362200-51373400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr12:51362200-51373800	Weak transcription	Placenta	Placenta
47	chr12:51362400-51376800	Weak transcription	Brain Hippocampus Middle	brain
48	chr12:51362400-51378600	Weak transcription	NH-A	brain
49	chr12:51362400-51382000	Weak transcription	Lung	lung
50	chr12:51362600-51366200	Strong transcription	Primary monocytes fromperipheralblood	blood

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