Variant report

Variant	rs11183479
Chromosome Location	chr12:46824164-46824165
allele	C/T
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:12)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46765214..46768254-chr12:46823583..46826373,3	MCF-7	breast:
2	chr12:46771601..46773692-chr12:46823826..46825790,2	K562	blood:
3	chr12:46785131..46787276-chr12:46823023..46825846,2	K562	blood:
4	chr12:46774613..46778148-chr12:46823214..46828002,7	K562	blood:
5	chr12:46824063..46826118-chr12:47049459..47052232,2	K562	blood:
6	chr12:46822440..46824303-chr12:46827711..46830028,2	K562	blood:
7	chr12:46760616..46768014-chr12:46824033..46835241,16	K562	blood:
8	chr12:46822289..46824421-chr12:46826124..46828179,2	MCF-7	breast:
9	chr12:46775635..46778663-chr12:46823030..46824747,3	MCF-7	breast:
10	chr12:46788936..46790826-chr12:46823903..46825881,2	K562	blood:
11	chr12:46769817..46771459-chr12:46823347..46825693,2	K562	blood:
12	chr12:46650913..46653725-chr12:46822184..46824848,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC38A2-1	chr12:46824119-46824219	XLOC_010061

No data

Variant related genes	Relation type
ENSG00000258096	Chromatin interaction
ENSG00000257261	Chromatin interaction
ENSG00000134294	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10748448	0.82[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10748450	0.87[EUR][1000 genomes]
rs10785627	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10785628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs10785629	0.87[EUR][1000 genomes]
rs10880966	0.86[AMR][1000 genomes]
rs10880967	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10880968	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10880969	0.86[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880970	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10880971	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10880973	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11183456	1.00[CHB][hapmap]
rs11183478	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11183483	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11183484	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11183486	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11183488	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11183503	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11183504	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1125909	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11561535	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11837427	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12099669	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12298616	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12314541	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12319162	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12813763	0.90[AMR][1000 genomes]
rs12814298	0.84[AMR][1000 genomes]
rs12814341	0.90[AMR][1000 genomes]
rs12822345	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12824565	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12832425	0.90[AMR][1000 genomes]
rs12832777	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1472179	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1492895	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2045556	0.89[CHB][hapmap]
rs2131371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2220727	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2408497	0.85[AMR][1000 genomes]
rs2408498	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2897951	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3936214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4072304	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4076247	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4077707	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs4077708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs4258438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4427617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4768118	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4768119	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4768121	0.86[AMR][1000 genomes]
rs4768122	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs4768699	0.82[CEU][hapmap]
rs4768709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4768710	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4768711	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4768712	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4768713	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4768714	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4768715	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4768716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768717	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4768718	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4768719	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4768723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs4768724	0.87[EUR][1000 genomes]
rs4768725	0.87[EUR][1000 genomes]
rs4768726	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4768728	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4768729	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6582641	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6582642	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6582643	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6582645	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6582646	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6582657	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6582658	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6582659	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7134289	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7301001	0.86[AMR][1000 genomes]
rs7311504	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7312259	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7485580	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7485599	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7486495	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7486532	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7486580	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7486596	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7487828	0.91[AMR][1000 genomes]
rs7487877	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7488450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7488577	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7489242	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959731	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7968897	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7976280	0.85[AMR][1000 genomes]
rs7980455	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9669404	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9706162	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9971879	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46820000-46830600	Weak transcription	Ovary	ovary
2	chr12:46820400-46825000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:46821200-46824200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr12:46821600-46824200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr12:46821600-46827600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:46821600-46848600	Weak transcription	Primary B cells from cord blood	blood
7	chr12:46822200-46824200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:46822400-46825800	Enhancers	Dnd41	blood
9	chr12:46822400-46826800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:46822400-46833600	Enhancers	Hela-S3	cervix
11	chr12:46822800-46826600	Enhancers	NHDF-Ad	bronchial
12	chr12:46823000-46824200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr12:46823000-46824200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:46823000-46826600	Enhancers	HMEC	breast
15	chr12:46823200-46824200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:46823200-46824200	Weak transcription	Fetal Heart	heart
17	chr12:46823200-46824200	Enhancers	HepG2	liver
18	chr12:46823200-46825200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:46823400-46825800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:46823400-46826400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:46823400-46826400	Enhancers	NHLF	lung
22	chr12:46823400-46826600	Enhancers	Osteobl	bone
23	chr12:46823600-46824200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:46823600-46824400	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr12:46823600-46824600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:46823600-46824800	Flanking Active TSS	A549	lung
27	chr12:46823600-46825200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:46823600-46825600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:46823600-46826400	Enhancers	HSMM	muscle
30	chr12:46823600-46826600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr12:46823800-46824600	Weak transcription	Stomach Mucosa	stomach
32	chr12:46823800-46825000	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr12:46824000-46824200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:46824000-46824200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:46824000-46824200	Active TSS	GM12878-XiMat	blood
36	chr12:46824000-46824200	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr12:46824000-46824400	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr12:46824000-46824400	Active TSS	Liver	Liver
39	chr12:46824000-46824600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:46824000-46824600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:46824000-46824600	Enhancers	Primary T cells from cord blood	blood
42	chr12:46824000-46824600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr12:46824000-46824600	Flanking Active TSS	K562	blood
44	chr12:46824000-46824800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:46824000-46824800	Flanking Active TSS	HUVEC	blood vessel
46	chr12:46824000-46824800	Flanking Active TSS	NH-A	brain
47	chr12:46824000-46824800	Flanking Active TSS	NHEK	skin
48	chr12:46824000-46825000	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr12:46824000-46825000	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr12:46824000-46825000	Enhancers	Fetal Intestine Large	intestine

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