Variant report

Variant	rs416062
Chromosome Location	chr12:51412500-51412501
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51408168..51409685-chr12:51411443..51413744,2	K562	blood:
2	chr12:51404293..51409685-chr12:51411834..51415817,7	K562	blood:
3	chr12:51399342..51401047-chr12:51411160..51415071,3	MCF-7	breast:
4	chr12:51410218..51413195-chr12:51416479..51420227,4	MCF-7	breast:
5	chr12:51157130..51159042-chr12:51410041..51412870,2	K562	blood:
6	chr12:51408556..51414296-chr12:51415375..51421759,13	MCF-7	breast:
7	chr12:51412418..51415100-chr12:51610730..51614429,3	K562	blood:
8	chr12:51403352..51405981-chr12:51411330..51414858,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272028	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000184271	Chromatin interaction
ENSG00000110911	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1026994	1.00[ASN][1000 genomes]
rs10747603	1.00[ASN][1000 genomes]
rs10783411	1.00[ASN][1000 genomes]
rs10783412	1.00[ASN][1000 genomes]
rs10876126	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169679	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12423207	0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs150909	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161044	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161045	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161046	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161047	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17229232	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029147	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046498	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs224564	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224566	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224569	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224570	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224573	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224574	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224576	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs224578	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224585	0.94[EUR][1000 genomes]
rs224586	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs224590	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs224592	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224593	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554858	0.86[AMR][1000 genomes]
rs2554859	0.91[AMR][1000 genomes]
rs2630358	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2630362	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630366	0.82[AMR][1000 genomes]
rs2630367	0.82[AMR][1000 genomes]
rs319930	0.82[AMR][1000 genomes]
rs319938	0.82[AMR][1000 genomes]
rs364627	0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390424	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394384	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4238110	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs435965	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs445520	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452587	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768875	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4768959	1.00[ASN][1000 genomes]
rs55874852	0.82[AMR][1000 genomes]
rs58309379	1.00[ASN][1000 genomes]
rs613977	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618510	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6580779	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580780	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580781	0.90[EUR][1000 genomes]
rs6580783	1.00[ASN][1000 genomes]
rs686528	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706803	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs706804	0.90[EUR][1000 genomes]
rs7299484	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968372	0.80[EUR][1000 genomes]
rs7969536	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969702	0.92[EUR][1000 genomes]
rs7971712	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972608	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974923	1.00[ASN][1000 genomes]
rs7975628	1.00[ASN][1000 genomes]
rs7977993	1.00[ASN][1000 genomes]
rs829021	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs853236	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9739943	0.92[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs416062	SLC11A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51386000-51414200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:51399200-51418000	Weak transcription	Gastric	stomach
3	chr12:51399800-51414600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:51399800-51415600	Weak transcription	Right Ventricle	heart
5	chr12:51401400-51417800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr12:51402000-51418000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:51402000-51418000	Weak transcription	Fetal Stomach	stomach
8	chr12:51402400-51415600	Weak transcription	GM12878-XiMat	blood
9	chr12:51402400-51417200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:51402400-51417600	Weak transcription	Left Ventricle	heart
11	chr12:51402400-51418000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:51403000-51418000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:51403400-51415600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:51403400-51417600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr12:51403600-51414200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr12:51403600-51414400	Weak transcription	Hela-S3	cervix
17	chr12:51403600-51414600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:51403600-51417400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:51403600-51417600	Weak transcription	HSMM	muscle
20	chr12:51403800-51412800	Weak transcription	Primary T cells from cord blood	blood
21	chr12:51403800-51412800	Weak transcription	Dnd41	blood
22	chr12:51403800-51417000	Weak transcription	Brain Germinal Matrix	brain
23	chr12:51404200-51414600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:51404800-51417800	Weak transcription	Fetal Brain Female	brain
25	chr12:51405800-51415000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr12:51406000-51414600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:51406000-51415200	Weak transcription	Right Atrium	heart
28	chr12:51406400-51417200	Weak transcription	Fetal Brain Male	brain
29	chr12:51406400-51417400	Weak transcription	Osteobl	bone
30	chr12:51406400-51417600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:51406600-51413800	Weak transcription	Brain Anterior Caudate	brain
32	chr12:51406800-51414200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr12:51406800-51415000	Weak transcription	Fetal Heart	heart
34	chr12:51407000-51412800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr12:51407000-51412800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr12:51407000-51414800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr12:51407000-51417400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:51407000-51417600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr12:51407000-51418000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:51407200-51415800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr12:51407400-51412800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:51407400-51412800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:51407400-51412800	Weak transcription	Brain Angular Gyrus	brain
44	chr12:51407400-51412800	Weak transcription	Brain Substantia Nigra	brain
45	chr12:51407400-51415200	Weak transcription	Placenta	Placenta
46	chr12:51407600-51413000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr12:51407600-51413000	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr12:51407600-51415200	Weak transcription	Lung	lung
49	chr12:51407600-51415600	Weak transcription	Small Intestine	intestine
50	chr12:51407600-51417200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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