Variant report

Variant	rs17046589
Chromosome Location	chr2:55237049-55237050
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55131786..55132384-chr2:55236584..55237394,2	MCF-7	breast:
2	chr2:55219389..55222736-chr2:55233484..55237490,3	MCF-7	breast:
3	chr2:55236989..55239116-chr2:55240470..55242602,2	K562	blood:

Variant related genes	Relation type
ENSG00000200086	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs13031431	1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs17046579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17046586	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1822617	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2255026	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2255393	0.85[CHB][hapmap]
rs2580768	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2580769	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2580770	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2580771	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2588513	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2588515	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2588516	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2588522	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2919126	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2920859	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2920892	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2968788	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972063	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2972092	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34352825	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34378852	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34928331	0.96[ASN][1000 genomes]
rs35981204	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4672003	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545464	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545465	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs6734314	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6739210	0.91[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72795434	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7355716	0.84[CHB][hapmap]

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	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55198200-55237200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
3	chr2:55223000-55237200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:55226600-55237200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:55227600-55239000	Weak transcription	Hela-S3	cervix
6	chr2:55229600-55237200	Weak transcription	Pancreas	Pancrea
7	chr2:55231000-55237400	Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr2:55231000-55238200	Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr2:55232200-55237200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:55232200-55244800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:55232400-55237200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:55233200-55237600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr2:55233200-55240400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:55233600-55237400	Active TSS	Fetal Muscle Leg	muscle
15	chr2:55233800-55237800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:55234600-55237200	Weak transcription	Small Intestine	intestine
17	chr2:55234800-55237200	Weak transcription	Dnd41	blood
18	chr2:55234800-55237400	Active TSS	Psoas Muscle	Psoas
19	chr2:55234800-55244800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:55234800-55246000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:55235000-55237400	Weak transcription	Fetal Heart	heart
22	chr2:55235000-55237400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr2:55235200-55237400	Active TSS	Fetal Intestine Large	intestine
24	chr2:55235400-55237200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:55235400-55237200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr2:55235400-55237200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:55235400-55237600	Active TSS	Fetal Intestine Small	intestine
28	chr2:55235400-55238000	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr2:55235600-55237200	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr2:55235600-55240600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:55236000-55237200	Active TSS	Liver	Liver
32	chr2:55236000-55237400	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr2:55236000-55238400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:55236200-55237800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:55236200-55238000	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr2:55236200-55239600	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr2:55236400-55237400	Active TSS	Thymus	Thymus
38	chr2:55236400-55237400	Active TSS	GM12878-XiMat	blood
39	chr2:55236400-55237600	Active TSS	Fetal Muscle Trunk	muscle
40	chr2:55236400-55238000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:55236400-55238800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr2:55236600-55237200	Active TSS	Fetal Thymus	thymus
43	chr2:55236600-55237200	Active TSS	Right Atrium	heart
44	chr2:55236600-55237200	Genic enhancers	K562	blood
45	chr2:55236600-55237400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:55236600-55237400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:55236600-55237400	Active TSS	Stomach Smooth Muscle	stomach
48	chr2:55236600-55237600	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr2:55236600-55237600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr2:55236600-55237600	Flanking Active TSS	Brain Angular Gyrus	brain

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