Variant report

Variant	rs12593446
Chromosome Location	chr15:56202069-56202070
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56199692..56201562-chr15:56202025..56204154,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10744958	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1134352	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11635063	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12594053	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12906680	0.82[EUR][1000 genomes]
rs12912488	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12912732	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1605837	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16976653	1.00[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs17819276	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17819294	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1912404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28444575	0.88[EUR][1000 genomes]
rs34552316	0.85[ASN][1000 genomes]
rs3759865	0.82[EUR][1000 genomes]
rs4774229	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493825	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6493827	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6493828	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7163864	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7180060	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7182280	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8042640	0.82[ASN][1000 genomes]
rs967128	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9920283	0.81[JPT][hapmap]

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	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv569542	chr15:56185262-56210929	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv528617	chr15:56202069-56207983	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12593446	RSL24D1	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56176000-56216200	Weak transcription	Fetal Intestine Small	intestine
2	chr15:56188400-56207800	Weak transcription	Primary T cells from cord blood	blood
3	chr15:56188600-56218400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr15:56190000-56220000	Weak transcription	Pancreas	Pancrea
5	chr15:56190200-56221200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:56190400-56219800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:56192400-56207800	Weak transcription	Liver	Liver
8	chr15:56192600-56209000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr15:56199200-56203600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:56199400-56202600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:56199400-56203800	Flanking Active TSS	A549	lung
12	chr15:56199800-56203600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:56200000-56202200	Enhancers	NH-A	brain
14	chr15:56200000-56202800	Enhancers	Osteobl	bone
15	chr15:56200000-56203200	Enhancers	HSMMtube	muscle
16	chr15:56200200-56202200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:56200200-56202800	Enhancers	NHDF-Ad	bronchial
18	chr15:56200200-56203600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr15:56200200-56208600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr15:56200200-56213200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:56200400-56202600	Enhancers	Hela-S3	cervix
22	chr15:56200400-56203600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:56200400-56209000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:56200600-56202200	Enhancers	NHLF	lung
25	chr15:56200600-56203200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr15:56200800-56202400	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr15:56200800-56203000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:56200800-56218000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr15:56201000-56230000	Weak transcription	Fetal Intestine Large	intestine
30	chr15:56201200-56202600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr15:56201200-56217200	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr15:56201400-56203600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:56201800-56202200	Flanking Active TSS	HMEC	breast
34	chr15:56201800-56205800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:56202000-56202200	Strong transcription	Primary hematopoietic stem cells	blood
36	chr15:56202000-56202400	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr15:56202000-56202400	Enhancers	HSMM	muscle
38	chr15:56202000-56202600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr15:56202000-56203200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:56202000-56203200	Active TSS	Psoas Muscle	Psoas
41	chr15:56202000-56203400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr15:56202000-56203600	Enhancers	NHEK	skin
43	chr15:56202000-56207000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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