Variant report

Variant	rs13386979
Chromosome Location	chr2:63579964-63579965
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10167849	0.91[CHB][hapmap]
rs10200678	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10206947	0.83[GIH][hapmap];0.81[LWK][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs11682642	0.91[CHB][hapmap];0.96[YRI][hapmap]
rs11687645	0.91[CHB][hapmap];0.96[YRI][hapmap]
rs11691192	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs11895059	0.91[CHB][hapmap];0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs11899838	0.82[GIH][hapmap]
rs11899999	0.91[CHB][hapmap];0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs12615652	0.91[CHB][hapmap];0.96[YRI][hapmap]
rs12615947	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];0.99[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12713486	0.91[CHB][hapmap]
rs12713488	0.91[CHB][hapmap];0.83[LWK][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12713489	0.81[ASN][1000 genomes]
rs12713490	0.91[CHB][hapmap];0.90[YRI][hapmap]
rs12713491	0.91[CHB][hapmap];0.90[YRI][hapmap];0.81[ASN][1000 genomes]
rs12988024	0.91[CHB][hapmap];0.89[YRI][hapmap];0.81[ASN][1000 genomes]
rs12988058	0.91[CHB][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs13021322	0.91[CHB][hapmap];0.93[YRI][hapmap]
rs13028443	0.91[CHB][hapmap];0.90[YRI][hapmap];0.81[ASN][1000 genomes]
rs13383251	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1356388	0.91[CHB][hapmap];0.96[YRI][hapmap]
rs1607201	0.91[CHB][hapmap];0.96[YRI][hapmap]
rs1829259	0.91[CHB][hapmap];0.82[YRI][hapmap]
rs1850985	0.84[GIH][hapmap]
rs1878507	0.91[CHB][hapmap];0.84[CHD][hapmap];0.90[YRI][hapmap];0.82[ASN][1000 genomes]
rs1922422	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs1996401	0.91[CHB][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2138796	0.91[CHB][hapmap];0.96[YRI][hapmap]
rs2138798	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2421885	0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[YRI][hapmap];0.82[ASN][1000 genomes]
rs3768677	0.91[CHB][hapmap];0.96[YRI][hapmap]
rs4316930	0.84[GIH][hapmap];0.88[LWK][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap]
rs4671463	0.87[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs4671465	0.86[GIH][hapmap]
rs4671486	0.81[ASN][1000 genomes]
rs4671492	0.91[CHB][hapmap];0.96[YRI][hapmap]
rs4671495	0.89[CHB][hapmap];0.85[YRI][hapmap]
rs4671496	0.91[CHB][hapmap];0.90[YRI][hapmap]
rs55687260	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6714258	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6718198	0.91[CHB][hapmap];0.89[YRI][hapmap];0.81[ASN][1000 genomes]
rs6758966	0.84[GIH][hapmap]
rs7355552	0.91[CHB][hapmap];0.89[YRI][hapmap]
rs7355671	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs7556900	0.84[ASN][1000 genomes]
rs7567098	0.81[ASN][1000 genomes]
rs7599208	0.91[CHB][hapmap];0.96[YRI][hapmap]
rs7608504	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs932173	0.91[CHB][hapmap];0.96[YRI][hapmap]
rs9808380	0.91[CHB][hapmap];0.80[LWK][hapmap];0.96[YRI][hapmap]
rs9808385	0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1006848	chr2:63061816-63631407	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Active TSS 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	15 gene(s)	inside rSNPs	diseases
3	nsv535768	chr2:63413596-63631407	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv1800788	chr2:63473443-63900292	ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv834241	chr2:63490262-63668205	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1014935	chr2:63545598-63599535	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1012628	chr2:63545598-63604859	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1013613	chr2:63545598-63606689	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13386979	NM_015910	cis	multi-tissue	Pritchard
rs13386979	C2orf86	cis	Liver	GTEx
rs13386979	VPS54	cis	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63567800-63585600	Weak transcription	Gastric	stomach
2	chr2:63571800-63580800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:63572000-63583000	Weak transcription	Primary T cells from cord blood	blood
4	chr2:63572000-63624000	Weak transcription	Left Ventricle	heart
5	chr2:63572600-63580200	Weak transcription	Ovary	ovary
6	chr2:63572800-63597000	Weak transcription	Dnd41	blood
7	chr2:63576800-63584600	Weak transcription	Brain Angular Gyrus	brain
8	chr2:63577600-63580800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:63578000-63583600	Weak transcription	Primary B cells from cord blood	blood
10	chr2:63578600-63582400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:63579800-63580000	ZNF genes & repeats	Stomach Smooth Muscle	stomach
12	chr2:63579800-63580800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
13	chr2:63579800-63581000	ZNF genes & repeats	Aorta	Aorta
14	chr2:63579800-63581000	Strong transcription	Fetal Stomach	stomach
15	chr2:63579800-63581400	Strong transcription	Adipose Nuclei	Adipose
16	chr2:63579800-63582200	Weak transcription	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links