Variant report

Variant	rs12438599
Chromosome Location	chr15:52973171-52973172
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:52972814-52973344	Raji	blood:	n/a	n/a
2	MEF2A	chr15:52972953-52973319	K562	blood:	n/a	chr15:52973121-52973136

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52819791..52821534-chr15:52970285..52973265,2	MCF-7	breast:
2	chr15:52967401..52973659-chr15:53000765..53004676,11	MCF-7	breast:
3	chr15:52968259..52973250-chr15:52997483..53005703,18	MCF-7	breast:
4	chr15:52966022..52968187-chr15:52971881..52974523,2	K562	blood:
5	chr15:52942408..52952117-chr15:52965431..52973600,32	MCF-7	breast:
6	chr15:52972928..52973805-chr6:11737938..11738770,2	MCF-7	breast:

No data

Variant related genes	Relation type
FAM214A	TF binding region
ENSG00000197535	Chromatin interaction
ENSG00000047346	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10851522	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12595161	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17651917	0.89[ASN][1000 genomes]
rs1991300	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73396772	0.92[ASN][1000 genomes]
rs73398904	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8026277	0.93[EUR][1000 genomes];0.95[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	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1049534	chr15:52903314-53022926	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52972000-52974000	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr15:52972000-52974800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr15:52972200-52974000	Enhancers	Fetal Heart	heart
4	chr15:52972200-52974200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr15:52972200-52974200	Enhancers	Liver	Liver
6	chr15:52972200-52974200	Flanking Active TSS	GM12878-XiMat	blood
7	chr15:52972400-52973400	Weak transcription	Primary T cells from cord blood	blood
8	chr15:52972400-52973400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr15:52972400-52974000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr15:52972400-52974000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr15:52972400-52974200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr15:52972400-52974200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr15:52972400-52974200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr15:52972400-52974200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr15:52972400-52974200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr15:52972400-52975000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr15:52972400-52975200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr15:52972400-52975200	Weak transcription	Fetal Thymus	thymus
19	chr15:52972600-52973200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:52972600-52973200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr15:52972600-52973600	Enhancers	HSMM	muscle
22	chr15:52972600-52974000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr15:52972600-52974000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr15:52972600-52974400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:52972600-52974400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:52972600-52974600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr15:52972800-52974200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr15:52973000-52973400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr15:52973000-52973400	Enhancers	HSMMtube	muscle
30	chr15:52973000-52974000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr15:52973000-52979200	Enhancers	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links