Variant report

Variant	rs13379947
Chromosome Location	chr15:62184801-62184802
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1000598	0.89[CEU][hapmap]
rs11071642	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs11631970	0.85[CEU][hapmap];0.84[MEX][hapmap]
rs11635569	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12437684	0.87[EUR][1000 genomes]
rs12439934	0.81[CEU][hapmap]
rs12708470	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs12901481	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs12906423	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12908081	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908182	0.84[EUR][1000 genomes]
rs12908472	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12911564	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12912208	0.85[CEU][hapmap]
rs12915295	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12915825	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916268	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379492	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1346035	0.82[EUR][1000 genomes]
rs1346037	0.82[EUR][1000 genomes]
rs1425270	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1436966	0.85[CEU][hapmap]
rs17205225	0.81[AMR][1000 genomes]
rs17271144	0.83[EUR][1000 genomes]
rs17271151	0.85[CEU][hapmap]
rs17271158	0.81[EUR][1000 genomes]
rs17271193	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17271340	0.85[CEU][hapmap]
rs1981916	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1981917	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414753	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs2414755	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28373613	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28411984	0.90[EUR][1000 genomes]
rs34965045	0.89[EUR][1000 genomes]
rs3743297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3784634	0.81[CEU][hapmap];0.86[GIH][hapmap]
rs3809517	0.84[CEU][hapmap]
rs4283171	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4587915	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4774422	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4774427	0.89[CEU][hapmap];0.92[GIH][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes]
rs4775453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7166891	0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7170293	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7172145	0.86[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7172967	0.88[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes]
rs7179506	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs748669	0.86[EUR][1000 genomes]
rs8029942	0.85[CEU][hapmap]
rs8032681	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033816	0.81[TSI][hapmap]
rs8034185	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs8034216	0.85[CEU][hapmap];0.89[GIH][hapmap];0.81[EUR][1000 genomes]
rs8034335	0.85[CEU][hapmap];0.92[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs8034914	0.86[GIH][hapmap]
rs8039105	0.85[CEU][hapmap]
rs963024	0.89[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9920015	0.80[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904284	chr15:62123600-62243197	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv521334	chr15:62129809-62340126	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv527451	chr15:62129809-62340126	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv904285	chr15:62146598-62246864	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv904286	chr15:62146598-62313373	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv904287	chr15:62146598-62338797	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv904288	chr15:62146598-62356386	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv569641	chr15:62155282-62287456	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv904289	chr15:62156690-62287456	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv516639	chr15:62175134-62340126	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv904290	chr15:62175134-62356386	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv569642	chr15:62178695-62243197	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv904291	chr15:62178695-62287456	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv904292	chr15:62178695-62313373	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv904293	chr15:62178695-62338797	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv904294	chr15:62178695-62356386	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
17	nsv457176	chr15:62178695-62519658	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
18	nsv569643	chr15:62178695-62519658	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13379947	VPS13C	cis	cerebellum	SCAN
rs13379947	TPM1	cis	cerebellum	SCAN
rs13379947	CA12	cis	cerebellum	SCAN
rs13379947	FAM81A	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62139800-62185200	Weak transcription	NHLF	lung
2	chr15:62142000-62209400	Weak transcription	Colonic Mucosa	Colon
3	chr15:62142400-62253000	Weak transcription	Spleen	Spleen
4	chr15:62142600-62209200	Weak transcription	K562	blood
5	chr15:62143800-62235600	Weak transcription	Fetal Brain Male	brain
6	chr15:62144000-62194600	Weak transcription	Fetal Lung	lung
7	chr15:62146800-62230000	Weak transcription	Pancreas	Pancrea
8	chr15:62149000-62198000	Weak transcription	Fetal Kidney	kidney
9	chr15:62150000-62276200	Weak transcription	Psoas Muscle	Psoas
10	chr15:62150200-62185400	Weak transcription	Fetal Heart	heart
11	chr15:62153200-62185400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr15:62153800-62185000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr15:62154200-62198200	Weak transcription	NH-A	brain
14	chr15:62162600-62195200	Weak transcription	Fetal Stomach	stomach
15	chr15:62163000-62198400	Weak transcription	Osteobl	bone
16	chr15:62163800-62185400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr15:62165400-62185000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:62165600-62185400	Weak transcription	Gastric	stomach
19	chr15:62165600-62198400	Weak transcription	Thymus	Thymus
20	chr15:62172600-62185200	Weak transcription	HepG2	liver
21	chr15:62173400-62198200	Weak transcription	Left Ventricle	heart
22	chr15:62179400-62185200	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr15:62180200-62185200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr15:62180200-62185200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr15:62180200-62185800	Strong transcription	Duodenum Mucosa	Duodenum
26	chr15:62180400-62185000	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr15:62180400-62185200	Strong transcription	Dnd41	blood
28	chr15:62180800-62185800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr15:62181600-62185400	Strong transcription	Liver	Liver
30	chr15:62181800-62186000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr15:62181800-62198800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr15:62182600-62185000	Weak transcription	Brain Substantia Nigra	brain
33	chr15:62182600-62185200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr15:62182600-62185200	Weak transcription	HSMMtube	muscle
35	chr15:62182600-62185400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr15:62182600-62197200	Weak transcription	HSMM	muscle
37	chr15:62182600-62198400	Weak transcription	Fetal Thymus	thymus
38	chr15:62182800-62185000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:62183000-62185200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr15:62183000-62185200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr15:62183000-62198200	Weak transcription	HUVEC	blood vessel
42	chr15:62183800-62185200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
43	chr15:62183800-62185200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr15:62184000-62185000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr15:62184000-62185600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
46	chr15:62184000-62185600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:62184000-62185600	Strong transcription	Rectal Smooth Muscle	rectum
48	chr15:62184000-62186400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
49	chr15:62184000-62187600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:62184000-62190000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links