Variant report

Variant	rs13189229
Chromosome Location	chr5:118640853-118640854
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:118604371..118606788-chr5:118640818..118642448,2	K562	blood:
2	chr5:118622873..118625111-chr5:118638258..118641948,4	MCF-7	breast:
3	chr5:118604371..118606578-chr5:118640818..118642432,2	K562	blood:

Variant related genes	Relation type
ENSG00000145779	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10519579	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13153732	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13164306	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13171443	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13172873	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13172935	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13180238	0.84[EUR][1000 genomes]
rs1394630	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1465396	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17145124	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17145129	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17145142	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2012594	1.00[EUR][1000 genomes]
rs34016408	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34207529	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34692285	1.00[EUR][1000 genomes]
rs34902535	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35067404	1.00[EUR][1000 genomes]
rs35113297	1.00[EUR][1000 genomes]
rs35263427	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35605034	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35623432	0.90[EUR][1000 genomes]
rs35834554	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35956442	1.00[EUR][1000 genomes]
rs35981322	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55810506	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs56840858	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57001486	0.95[EUR][1000 genomes]
rs58196366	1.00[EUR][1000 genomes]
rs59085117	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60474651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61179451	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61366292	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61643326	1.00[EUR][1000 genomes]
rs6595180	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66540474	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67136651	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6866644	0.81[YRI][hapmap];0.80[AFR][1000 genomes]
rs6874081	1.00[EUR][1000 genomes]
rs6897744	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71585210	0.95[EUR][1000 genomes]
rs71585211	0.84[EUR][1000 genomes]
rs73252330	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73791001	0.83[ASN][1000 genomes]
rs7705109	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs999275	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757136	chr5:118555863-118667748	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	esv2759374	chr5:118555863-118667748	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1024648	chr5:118608175-118678268	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv869828	chr5:118610548-118691190	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118628000-118641000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:118635400-118643800	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr5:118635800-118641000	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr5:118635800-118641400	Enhancers	Thymus	Thymus
5	chr5:118636000-118641400	Enhancers	NHEK	skin
6	chr5:118636000-118641800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:118636200-118644000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr5:118636400-118644200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr5:118636400-118647000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr5:118636600-118641400	Enhancers	Primary B cells from peripheral blood	blood
11	chr5:118636800-118641800	Enhancers	HMEC	breast
12	chr5:118637000-118641200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:118637000-118653200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr5:118637200-118641200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:118637600-118641000	Enhancers	NH-A	brain
16	chr5:118638800-118649400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:118639200-118641400	Weak transcription	Esophagus	oesophagus
18	chr5:118639200-118641600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr5:118639200-118642000	Enhancers	Hela-S3	cervix
20	chr5:118639200-118643600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr5:118639200-118643800	Weak transcription	Small Intestine	intestine
22	chr5:118639200-118644000	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr5:118639200-118644200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr5:118639200-118644200	Weak transcription	Fetal Muscle Leg	muscle
25	chr5:118639200-118645800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:118639200-118649600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr5:118639200-118657200	Weak transcription	Lung	lung
28	chr5:118639200-118658400	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr5:118639400-118641000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:118639400-118641000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr5:118639400-118641400	Enhancers	Osteobl	bone
32	chr5:118639400-118641600	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr5:118639400-118641600	Weak transcription	Gastric	stomach
34	chr5:118639400-118644600	Weak transcription	HSMMtube	muscle
35	chr5:118639400-118646000	Weak transcription	Fetal Stomach	stomach
36	chr5:118639400-118653800	Weak transcription	Fetal Kidney	kidney
37	chr5:118639600-118641400	Enhancers	HepG2	liver
38	chr5:118639600-118643600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr5:118639600-118643800	Enhancers	Primary T cells from cord blood	blood
40	chr5:118639600-118644000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr5:118639600-118657000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr5:118640000-118642400	Genic enhancers	Primary T cells fromperipheralblood	blood
43	chr5:118640200-118641000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr5:118640200-118641400	Weak transcription	Pancreas	Pancrea
45	chr5:118640200-118642400	Genic enhancers	Primary B cells from cord blood	blood
46	chr5:118640200-118643400	Weak transcription	Fetal Lung	lung
47	chr5:118640200-118644000	Weak transcription	Placenta	Placenta
48	chr5:118640200-118645400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr5:118640400-118641200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr5:118640400-118641200	Enhancers	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links