Variant report

Variant	rs161046
Chromosome Location	chr12:51392252-51392253
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	chr12:51390934..51393083-chr12:51417005..51419912,3	K562	blood:

Variant related genes	Relation type
ENSG00000110911	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

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[JPT][hapmap];0.96[YRI][hapmap];1.00[ASN][1000 genomes]
rs10876126	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1095997	0.95[AMR][1000 genomes]
rs11169679	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169718	1.00[JPT][hapmap]
rs11169724	1.00[JPT][hapmap]
rs12369066	1.00[JPT][hapmap]
rs12423207	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs150909	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161044	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161045	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161047	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17125367	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs17125370	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs17125416	1.00[JPT][hapmap]
rs17125418	1.00[JPT][hapmap]
rs17125428	1.00[JPT][hapmap]
rs17229232	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2029147	1.00[ASN][1000 genomes]
rs2046498	0.82[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs224564	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224566	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224569	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224570	1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224573	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224574	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224576	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs224578	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224585	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs224586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs224590	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs224592	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224593	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554858	0.86[AMR][1000 genomes]
rs2554859	0.90[AMR][1000 genomes]
rs2554861	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2630353	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2630358	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2630362	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630366	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2630367	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs319930	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs319938	0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs319941	0.83[AMR][1000 genomes]
rs319943	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs319944	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs364627	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390424	1.00[CEU][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394384	1.00[CEU][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs416062	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4238110	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs435965	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs445520	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452587	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768875	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4768959	1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[ASN][1000 genomes]
rs4768973	1.00[JPT][hapmap]
rs55874852	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58309379	1.00[ASN][1000 genomes]
rs613977	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618510	0.88[EUR][1000 genomes]
rs6580779	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580780	1.00[CEU][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580781	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6580783	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs686528	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706803	0.82[CEU][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs706804	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7138860	0.82[EUR][1000 genomes]
rs7299484	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960097	1.00[JPT][hapmap]
rs7969536	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969702	0.88[EUR][1000 genomes]
rs7971712	0.82[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972608	0.82[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7974923	1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7975117	0.86[AMR][1000 genomes]
rs7975628	1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7977993	1.00[ASN][1000 genomes]
rs7978782	0.95[YRI][hapmap]
rs829016	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs829021	0.82[CEU][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs853236	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9739943	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs161046	SLC11A2	Cis_1M	lymphoblastoid	RTeQTL
rs161046	SLC11A2	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51378000-51401800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr12:51378600-51393200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:51378600-51399000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:51378800-51396000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:51379400-51396000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr12:51379400-51396200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr12:51379600-51395600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr12:51379800-51394600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:51379800-51396400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:51380000-51396200	Strong transcription	Dnd41	blood
11	chr12:51380200-51396400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:51380200-51396600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:51380200-51401800	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr12:51380200-51402200	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr12:51380400-51396200	Strong transcription	Fetal Brain Female	brain
16	chr12:51380400-51396200	Strong transcription	Placenta	Placenta
17	chr12:51380600-51399600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:51381200-51395800	Strong transcription	Primary B cells from peripheral blood	blood
19	chr12:51381200-51402200	Strong transcription	Fetal Thymus	thymus
20	chr12:51381200-51402200	Weak transcription	Psoas Muscle	Psoas
21	chr12:51381200-51402400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr12:51381200-51403000	Strong transcription	Fetal Muscle Leg	muscle
23	chr12:51381400-51394200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr12:51381400-51396400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr12:51381400-51403000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr12:51381800-51401600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr12:51381800-51401600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:51381800-51402400	Strong transcription	Liver	Liver
29	chr12:51382000-51394600	Strong transcription	Lung	lung
30	chr12:51382000-51395800	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr12:51382000-51396400	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr12:51382000-51402000	Strong transcription	Fetal Stomach	stomach
33	chr12:51382000-51402200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:51382400-51399400	Strong transcription	Fetal Intestine Large	intestine
35	chr12:51382600-51399400	Strong transcription	Fetal Intestine Small	intestine
36	chr12:51383000-51393000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:51384000-51394600	Strong transcription	HepG2	liver
38	chr12:51385600-51402600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr12:51386000-51406600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:51386000-51414200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr12:51386200-51398800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr12:51386800-51402200	Weak transcription	Right Atrium	heart
43	chr12:51387000-51396200	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr12:51387200-51392600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr12:51387800-51394000	Strong transcription	Osteobl	bone
46	chr12:51388000-51395800	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr12:51388000-51401000	Strong transcription	Primary T cells from cord blood	blood
48	chr12:51388200-51394200	Strong transcription	Primary hematopoietic stem cells	blood
49	chr12:51388200-51394200	Strong transcription	A549	lung
50	chr12:51388200-51396200	Strong transcription	Brain Substantia Nigra	brain

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