Variant report

Variant	rs8031427
Chromosome Location	chr15:40977176-40977177
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 27 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1051482	0.92[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10851396	0.87[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]
rs11070279	0.87[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]
rs11070290	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11852479	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11855517	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11857247	0.87[CEU][hapmap];0.94[MEX][hapmap]
rs12148185	0.92[CEU][hapmap];0.88[CHB][hapmap];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12898552	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12906755	0.81[CEU][hapmap]
rs12907448	0.90[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12907984	0.82[AMR][1000 genomes]
rs12908114	0.87[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]
rs12908443	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12910784	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12915563	0.83[CEU][hapmap];0.88[CHB][hapmap]
rs12916323	0.87[CEU][hapmap]
rs1453183	0.92[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]
rs17747399	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2010300	0.92[CEU][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes]
rs2289219	0.92[CEU][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs2304583	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2412545	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899000	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs34621344	0.83[EUR][1000 genomes]
rs34988257	0.86[EUR][1000 genomes]
rs35884042	0.82[AMR][1000 genomes]
rs36094699	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3759796	0.83[EUR][1000 genomes]
rs4457966	0.91[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs45592734	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5030783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62019934	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8025458	0.92[CEU][hapmap];1.00[MEX][hapmap]
rs8028910	0.87[CEU][hapmap]
rs8038396	0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9806410	0.91[CEU][hapmap]
rs999197	0.87[CEU][hapmap]

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	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv904099	chr15:40949526-41041875	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv529030	chr15:40956471-41012695	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv904100	chr15:40959624-40994706	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:27)

SNP	Gene	Cis/trans	Tissue	Source
rs8031427	C15orf57	cis	Muscle Skeletal	GTEx
rs8031427	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs8031427	C15orf57	cis	parietal	SCAN
rs8031427	CCDC32	cis	multi-tissue	Pritchard
rs8031427	RP11-111A22.1	cis	lung	GTEx
rs8031427	C15orf57	cis	Artery Aorta	GTEx
rs8031427	C15orf57	cis	lymphoblastoid	seeQTL
rs8031427	ZFYVE19	cis	cerebellum	SCAN
rs8031427	C15orf57	cis	Artery Tibial	GTEx
rs8031427	ZFYVE19	cis	parietal	SCAN
rs8031427	RAD51	cis	multi-tissue	Pritchard
rs8031427	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs8031427	C15orf57	cis	Esophagus Mucosa	GTEx
rs8031427	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs8031427	ZFYVE19	cis	multi-tissue	Pritchard
rs8031427	RP11-111A22.1	cis	Artery Tibial	GTEx
rs8031427	C15orf57	cis	lung	GTEx
rs8031427	IVD	cis	cerebellum	SCAN
rs8031427	C15orf23	cis	parietal	SCAN
rs8031427	C15orf57	cis	Stomach	GTEx
rs8031427	C15orf57	cis	Nerve Tibial	GTEx
rs8031427	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs8031427	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs8031427	C15orf57	cis	Esophagus Muscularis	GTEx
rs8031427	C15orf23	cis	cerebellum	SCAN
rs8031427	C15orf57	cis	Adipose Subcutaneous	GTEx
rs8031427	C15orf57	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40913800-40986000	Weak transcription	A549	lung
2	chr15:40945000-40984200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:40950000-40981200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:40955200-40983200	Weak transcription	Fetal Intestine Small	intestine
5	chr15:40958600-40981000	Weak transcription	Thymus	Thymus
6	chr15:40971200-40985800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:40971400-40977400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:40971400-40981000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:40971600-40984000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:40971600-40984200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr15:40971600-40985600	Weak transcription	Dnd41	blood
12	chr15:40971600-40985800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr15:40971800-40982400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr15:40971800-40983800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr15:40971800-40984000	Weak transcription	Brain Hippocampus Middle	brain
16	chr15:40971800-40984200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr15:40971800-40985800	Weak transcription	Brain Angular Gyrus	brain
18	chr15:40972400-40984600	Weak transcription	Placenta	Placenta
19	chr15:40972600-40984200	Weak transcription	Spleen	Spleen
20	chr15:40972800-40984000	Weak transcription	HepG2	liver
21	chr15:40973200-40985600	Weak transcription	Primary B cells from cord blood	blood
22	chr15:40973400-40985800	Weak transcription	GM12878-XiMat	blood
23	chr15:40973600-40984000	Weak transcription	Primary B cells from peripheral blood	blood
24	chr15:40976200-40982800	Weak transcription	Fetal Stomach	stomach
25	chr15:40976200-40984000	Weak transcription	Primary T cells from cord blood	blood
26	chr15:40976400-40977200	Enhancers	NHEK	skin
27	chr15:40976400-40977400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:40976400-40984000	Weak transcription	Brain Anterior Caudate	brain
29	chr15:40976600-40977200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:40976600-40977200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:40976800-40977200	Enhancers	HMEC	breast
32	chr15:40977000-40978000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:40977000-40978200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr15:40977000-40985800	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links