Variant report

Variant	rs224589
Chromosome Location	chr12:51399050-51399051
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51397137..51401396-chr12:51418750..51422923,7	MCF-7	breast:
2	chr12:51397939..51400659-chr12:51662476..51664122,2	MCF-7	breast:
3	chr12:51396990..51399929-chr12:51402029..51404417,2	K562	blood:
4	chr12:51397706..51399283-chr12:51631640..51634550,2	MCF-7	breast:
5	chr12:51398011..51404686-chr12:51416862..51423754,14	MCF-7	breast:
6	chr12:51397752..51401111-chr12:51474159..51477147,3	MCF-7	breast:
7	chr12:51397539..51404278-chr12:51405080..51409503,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110911	Chromatin interaction
ENSG00000170545	Chromatin interaction
ENSG00000110925	Chromatin interaction
ENSG00000272028	Chromatin interaction
ENSG00000183283	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1005559	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs1048230	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs10506298	0.87[ASN][1000 genomes]
rs10506299	0.87[ASN][1000 genomes]
rs11169626	0.85[ASN][1000 genomes]
rs11169633	0.85[ASN][1000 genomes]
rs11169636	0.82[ASN][1000 genomes]
rs11169637	0.85[ASN][1000 genomes]
rs11169639	0.85[ASN][1000 genomes]
rs11169641	0.85[ASN][1000 genomes]
rs11169642	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs11169644	0.86[ASN][1000 genomes]
rs11169646	0.82[ASN][1000 genomes]
rs11169647	0.85[ASN][1000 genomes]
rs11169648	0.87[ASN][1000 genomes]
rs11169649	0.87[ASN][1000 genomes]
rs11169652	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs11169654	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11169655	0.87[ASN][1000 genomes]
rs11169661	0.93[ASN][1000 genomes]
rs11169667	0.86[CHB][hapmap];0.93[ASN][1000 genomes]
rs11169669	0.91[ASN][1000 genomes]
rs11169670	0.93[ASN][1000 genomes]
rs11169671	0.93[ASN][1000 genomes]
rs11169672	0.90[ASN][1000 genomes]
rs11519977	0.87[ASN][1000 genomes]
rs12366476	0.85[ASN][1000 genomes]
rs12366756	0.86[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs12369278	0.85[ASN][1000 genomes]
rs12369639	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12369658	0.85[ASN][1000 genomes]
rs12369666	0.85[ASN][1000 genomes]
rs12371463	0.85[ASN][1000 genomes]
rs12372173	0.90[ASN][1000 genomes]
rs12809563	0.85[ASN][1000 genomes]
rs12810659	0.87[ASN][1000 genomes]
rs12811777	0.85[ASN][1000 genomes]
rs12812727	0.85[ASN][1000 genomes]
rs12813728	0.85[ASN][1000 genomes]
rs12817386	0.87[ASN][1000 genomes]
rs12818033	0.85[ASN][1000 genomes]
rs12819296	0.85[ASN][1000 genomes]
rs12821444	0.85[ASN][1000 genomes]
rs12824840	0.85[ASN][1000 genomes]
rs12824958	1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs12827861	0.90[ASN][1000 genomes]
rs12828536	0.90[ASN][1000 genomes]
rs12830048	0.87[ASN][1000 genomes]
rs12830073	0.90[ASN][1000 genomes]
rs12830422	0.84[ASN][1000 genomes]
rs12831269	0.93[ASN][1000 genomes]
rs12831597	0.83[ASN][1000 genomes]
rs15897	0.87[ASN][1000 genomes]
rs17125137	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs224565	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs224577	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs224591	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285228	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2285230	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2301529	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2516742	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2630364	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs319932	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34514224	0.85[ASN][1000 genomes]
rs35037088	0.85[ASN][1000 genomes]
rs35262273	0.85[ASN][1000 genomes]
rs35379220	0.85[ASN][1000 genomes]
rs35656976	0.87[ASN][1000 genomes]
rs35999440	0.85[ASN][1000 genomes]
rs407135	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422637	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs422982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs440595	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4444142	0.80[ASN][1000 genomes]
rs4471501	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs454520	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67025973	0.85[ASN][1000 genomes]
rs67133203	0.90[ASN][1000 genomes]
rs67259551	0.87[ASN][1000 genomes]
rs706801	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs706802	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71445768	0.85[ASN][1000 genomes]
rs71445772	0.82[ASN][1000 genomes]
rs7305638	0.85[ASN][1000 genomes]
rs7306293	0.85[ASN][1000 genomes]
rs73090655	0.85[ASN][1000 genomes]
rs7488909	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7959075	0.85[ASN][1000 genomes]
rs7959082	0.85[ASN][1000 genomes]
rs7965566	0.85[ASN][1000 genomes]
rs7972406	0.90[ASN][1000 genomes]
rs7975147	0.90[ASN][1000 genomes]
rs829022	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853235	0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs224589	SLC11A2	Cis_1M	lymphoblastoid	RTeQTL
rs224589	DDN	cis	cerebellum	SCAN
rs224589	CSRNP2	cis	cerebellum	SCAN
rs224589	SLC11A2	cis	lymphoblastoid	seeQTL
rs224589	TFCP2	cis	cerebellum	SCAN
rs224589	LETMD1	Cis_1M	lymphoblastoid	RTeQTL

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	chr12:51380200-51401800	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr12:51380200-51402200	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr12:51380600-51399600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:51381200-51402200	Strong transcription	Fetal Thymus	thymus
6	chr12:51381200-51402200	Weak transcription	Psoas Muscle	Psoas
7	chr12:51381200-51402400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr12:51381200-51403000	Strong transcription	Fetal Muscle Leg	muscle
9	chr12:51381400-51403000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:51381800-51401600	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr12:51381800-51401600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:51381800-51402400	Strong transcription	Liver	Liver
13	chr12:51382000-51402000	Strong transcription	Fetal Stomach	stomach
14	chr12:51382000-51402200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:51382400-51399400	Strong transcription	Fetal Intestine Large	intestine
16	chr12:51382600-51399400	Strong transcription	Fetal Intestine Small	intestine
17	chr12:51385600-51402600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr12:51386000-51406600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:51386000-51414200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr12:51386800-51402200	Weak transcription	Right Atrium	heart
21	chr12:51388000-51401000	Strong transcription	Primary T cells from cord blood	blood
22	chr12:51388200-51402000	Strong transcription	Adipose Nuclei	Adipose
23	chr12:51388600-51406600	Weak transcription	Small Intestine	intestine
24	chr12:51389400-51405400	Weak transcription	Esophagus	oesophagus
25	chr12:51390000-51400400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:51390000-51405800	Weak transcription	Stomach Mucosa	stomach
27	chr12:51390800-51402800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:51391000-51402200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr12:51391400-51399600	Weak transcription	Pancreas	Pancrea
30	chr12:51392400-51401800	Strong transcription	Thymus	Thymus
31	chr12:51392600-51402400	Strong transcription	Duodenum Mucosa	Duodenum
32	chr12:51393000-51402000	Strong transcription	Fetal Muscle Trunk	muscle
33	chr12:51393400-51402000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:51394400-51402400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:51394400-51403600	Weak transcription	Ovary	ovary
36	chr12:51395200-51402400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:51395400-51402600	Weak transcription	Fetal Brain Male	brain
38	chr12:51395600-51400200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr12:51396000-51402200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:51396000-51402400	Strong transcription	Left Ventricle	heart
41	chr12:51396800-51401600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:51396800-51402400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:51397400-51403000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr12:51397600-51399600	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr12:51397600-51400200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:51397600-51400400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr12:51397600-51400400	Strong transcription	Hela-S3	cervix
48	chr12:51397600-51400400	Strong transcription	Osteobl	bone
49	chr12:51397600-51401800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:51397600-51402000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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