Variant report

Variant	rs12916573
Chromosome Location	chr15:76791779-76791780
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs11072599	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11072603	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1117367	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs1125932	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12148786	0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12148805	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12437627	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12438077	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12439484	0.83[JPT][hapmap]
rs12441247	0.84[ASN][1000 genomes]
rs12441433	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs12441550	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12443137	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12592171	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12592386	0.87[ASN][1000 genomes]
rs12592420	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12593751	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12594212	0.91[ASN][1000 genomes]
rs12594577	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12899871	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12900494	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12902174	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12902414	1.00[ASN][1000 genomes]
rs12907805	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12911987	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs12914005	0.93[ASN][1000 genomes]
rs12915248	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12917430	0.87[ASN][1000 genomes]
rs1587381	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1588961	0.93[ASN][1000 genomes]
rs17361504	0.83[JPT][hapmap]
rs17362383	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17363713	0.92[ASN][1000 genomes]
rs17364076	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17364330	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17460201	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17461634	0.93[ASN][1000 genomes]
rs1867197	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs1874944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1875884	0.86[ASN][1000 genomes]
rs1875885	0.86[ASN][1000 genomes]
rs1946650	0.83[ASN][1000 genomes]
rs1965492	0.90[ASN][1000 genomes]
rs2083762	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs2117369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2120107	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs2120108	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2164101	0.93[ASN][1000 genomes]
rs2404736	0.81[ASN][1000 genomes]
rs2404737	0.81[ASN][1000 genomes]
rs2404740	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs284895	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs34707035	1.00[AFR][1000 genomes]
rs3866543	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap]
rs4079681	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4633676	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886496	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4886799	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4886801	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4886813	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4886817	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs4886818	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4886825	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes]
rs56089215	0.90[ASN][1000 genomes]
rs56216512	0.86[ASN][1000 genomes]
rs56351018	0.84[ASN][1000 genomes]
rs58511211	0.84[ASN][1000 genomes]
rs58684938	0.86[ASN][1000 genomes]
rs59088060	0.83[ASN][1000 genomes]
rs66754747	0.84[ASN][1000 genomes]
rs66986092	1.00[ASN][1000 genomes]
rs67204011	0.83[ASN][1000 genomes]
rs67232575	0.92[ASN][1000 genomes]
rs67263359	1.00[ASN][1000 genomes]
rs67888330	0.92[ASN][1000 genomes]
rs67920045	0.99[ASN][1000 genomes]
rs7162455	0.90[ASN][1000 genomes]
rs7163946	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7164060	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7164813	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7165025	0.93[ASN][1000 genomes]
rs7174953	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7179142	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7342603	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7350777	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs7403276	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8025134	0.93[ASN][1000 genomes]
rs8030411	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8036703	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs8039545	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8043474	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9646213	0.86[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	nsv542438	chr15:76697056-76892157	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
2	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv904400	chr15:76772062-77085283	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12916573	C15orf17	cis	parietal	SCAN
rs12916573	ODF3L1	cis	parietal	SCAN
rs12916573	SCAPER	cis	cerebellum	SCAN
rs12916573	NRG4	cis	parietal	SCAN
rs12916573	SCAPER	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76725800-76812600	Weak transcription	Left Ventricle	heart
2	chr15:76763000-76795000	Weak transcription	Primary B cells from cord blood	blood
3	chr15:76785400-76799800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr15:76787800-76793200	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:76788000-76795200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr15:76788000-76796600	Weak transcription	HSMM	muscle
7	chr15:76788200-76795000	Weak transcription	Primary T cells from cord blood	blood
8	chr15:76788200-76798400	Weak transcription	Dnd41	blood
9	chr15:76788400-76793800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:76788400-76813600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr15:76788600-76792000	Weak transcription	Fetal Intestine Small	intestine
12	chr15:76789200-76796200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:76789200-76796200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:76789200-76796600	Weak transcription	Adipose Nuclei	Adipose
15	chr15:76789600-76796400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr15:76790000-76802000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:76790600-76796200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr15:76791000-76796200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr15:76791200-76806200	Weak transcription	Fetal Muscle Leg	muscle

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