Variant report

Variant	rs12439925
Chromosome Location	chr15:31599501-31599502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11070920	0.82[AFR][1000 genomes]
rs11070922	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11070938	0.97[ASN][1000 genomes]
rs11630449	0.81[MKK][hapmap];0.86[YRI][hapmap]
rs12439534	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12595077	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12899315	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2004566	0.95[ASN][1000 genomes]
rs2338700	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2338701	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2879243	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34784107	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4779516	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4779858	0.98[ASN][1000 genomes]
rs4779859	0.98[ASN][1000 genomes]
rs7175141	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8039367	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[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	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription 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 miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
5	nsv1052722	chr15:31261834-31609680	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv542315	chr15:31261834-31609680	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv932896	chr15:31292475-31730445	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
8	nsv903838	chr15:31452911-31672128	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	esv1815415	chr15:31483843-31697213	Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
10	esv34100	chr15:31496514-31792591	Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
11	nsv456747	chr15:31537496-31637996	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv568772	chr15:31537496-31637996	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv903840	chr15:31589970-31800149	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
14	esv1839818	chr15:31594828-31637996	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31589400-31601800	Enhancers	Fetal Muscle Leg	muscle
2	chr15:31590400-31600600	Enhancers	Brain Cingulate Gyrus	brain
3	chr15:31590600-31599600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr15:31590800-31600600	Enhancers	Brain Substantia Nigra	brain
5	chr15:31591400-31600600	Enhancers	Brain Anterior Caudate	brain
6	chr15:31591600-31600600	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr15:31591800-31601400	Enhancers	Fetal Brain Male	brain
8	chr15:31592000-31599800	Enhancers	Brain Angular Gyrus	brain
9	chr15:31592400-31601600	Enhancers	Spleen	Spleen
10	chr15:31592400-31602800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:31592800-31601800	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr15:31593000-31601200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:31593200-31602800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:31594200-31602800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:31594400-31600600	Enhancers	Stomach Mucosa	stomach
16	chr15:31594600-31603000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr15:31595000-31601400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:31596000-31600800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr15:31596200-31600400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:31596600-31600600	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr15:31596600-31600800	Weak transcription	Fetal Heart	heart
22	chr15:31596800-31600600	Weak transcription	Right Atrium	heart
23	chr15:31597000-31600800	Enhancers	HepG2	liver
24	chr15:31597000-31601800	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr15:31597200-31601400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:31597400-31599600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr15:31597400-31599800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr15:31597400-31600200	Enhancers	Left Ventricle	heart
29	chr15:31597400-31600400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr15:31597400-31601000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr15:31597600-31600000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr15:31597600-31600400	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr15:31597800-31600200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr15:31598000-31599800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
35	chr15:31598200-31599600	Bivalent Enhancer	Fetal Stomach	stomach
36	chr15:31598200-31600000	Flanking Active TSS	Brain Germinal Matrix	brain
37	chr15:31598200-31600200	Enhancers	Right Ventricle	heart
38	chr15:31598400-31599600	Enhancers	Placenta	Placenta
39	chr15:31598400-31600800	Enhancers	H9 Cell Line	embryonic stem cell
40	chr15:31598400-31601600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
41	chr15:31598800-31599600	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr15:31598800-31599800	Bivalent Enhancer	Adipose Nuclei	Adipose
43	chr15:31598800-31601000	Enhancers	Brain Hippocampus Middle	brain
44	chr15:31598800-31601400	Enhancers	GM12878-XiMat	blood
45	chr15:31598800-31601600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:31598800-31601600	Enhancers	Primary B cells from peripheral blood	blood
47	chr15:31598800-31601600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr15:31599000-31599600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:31599000-31599800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
50	chr15:31599000-31599800	Enhancers	Gastric	stomach

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