Variant report

Variant	rs12438938
Chromosome Location	chr15:54271416-54271417
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10518746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12438683	0.82[AMR][1000 genomes]
rs12439568	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12439591	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12439761	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12442829	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17664311	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17664323	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17664329	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17731753	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1841945	0.94[JPT][hapmap]
rs2061746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2243799	0.90[YRI][hapmap]
rs2616867	0.83[CEU][hapmap]
rs4776199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56081015	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56104040	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56314416	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8036689	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904223	chr15:53665247-54340070	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1052235	chr15:53677524-54618723	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv542388	chr15:53677524-54618723	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv904226	chr15:53883244-54458310	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv457144	chr15:53890362-54455757	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv569440	chr15:53890362-54455757	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv569441	chr15:53890362-54456754	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv457145	chr15:53890393-54456754	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv569442	chr15:53890393-54456754	Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv949528	chr15:54041154-54281981	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv817539	chr15:54132584-55095235	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv833011	chr15:54226235-54421567	Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv569491	chr15:54260920-54397493	Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv904229	chr15:54267610-54340070	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54269200-54277200	Active TSS	Aorta	Aorta
2	chr15:54269800-54274800	Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr15:54270000-54271600	Active TSS	Stomach Smooth Muscle	stomach
4	chr15:54270200-54271600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr15:54270200-54271800	Active TSS	Brain Angular Gyrus	brain
6	chr15:54270200-54273200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:54270400-54271600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:54270400-54271600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
9	chr15:54270400-54271800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr15:54270400-54274200	Active TSS	Fetal Brain Female	brain
11	chr15:54270600-54271800	Active TSS	Brain Anterior Caudate	brain
12	chr15:54270600-54271800	Active TSS	Fetal Brain Male	brain
13	chr15:54270600-54271800	Active TSS	Psoas Muscle	Psoas
14	chr15:54270600-54272000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
15	chr15:54270600-54273600	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr15:54270600-54273800	Active TSS	Fetal Lung	lung
17	chr15:54270800-54271800	Active TSS	Fetal Muscle Trunk	muscle
18	chr15:54270800-54274600	Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr15:54271000-54271600	Active TSS	Fetal Muscle Leg	muscle
20	chr15:54271200-54271600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:54271200-54271600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:54271200-54271600	Enhancers	Fetal Stomach	stomach
23	chr15:54271200-54271800	Active TSS	Brain Hippocampus Middle	brain
24	chr15:54271400-54271600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
25	chr15:54271400-54271600	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr15:54271400-54271600	Bivalent/Poised TSS	Fetal Kidney	kidney
27	chr15:54271400-54274000	Active TSS	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links