Variant report

Variant	rs4924490
Chromosome Location	chr15:40961371-40961372
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10467972	0.91[CEU][hapmap]
rs10744948	0.90[EUR][1000 genomes]
rs11070284	0.83[EUR][1000 genomes]
rs11070292	0.91[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1142468	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11633367	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11638204	0.83[EUR][1000 genomes]
rs11638742	1.00[YRI][hapmap]
rs11854763	0.83[EUR][1000 genomes]
rs12438182	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12438955	0.83[EUR][1000 genomes]
rs12708401	0.83[EUR][1000 genomes]
rs12899600	0.87[EUR][1000 genomes]
rs12911738	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12912058	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12912339	0.83[EUR][1000 genomes]
rs12915109	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12916082	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17747351	1.00[CEU][hapmap]
rs2278888	1.00[CEU][hapmap]
rs2304580	1.00[CEU][hapmap];0.85[LWK][hapmap]
rs2412541	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2619681	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs3092978	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs34285050	0.82[EUR][1000 genomes]
rs4417527	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4420508	0.83[EUR][1000 genomes]
rs45457497	0.87[EUR][1000 genomes]
rs4924472	1.00[YRI][hapmap]
rs4924478	1.00[YRI][hapmap]
rs4924484	0.82[EUR][1000 genomes]
rs4924487	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs4924488	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4924491	0.87[EUR][1000 genomes]
rs4924500	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6492957	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6492958	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7161938	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7167417	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7168873	0.87[EUR][1000 genomes]
rs7171260	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7176974	0.83[EUR][1000 genomes]
rs7177192	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7178486	0.83[EUR][1000 genomes]
rs8028999	1.00[CEU][hapmap]
rs8031057	0.81[EUR][1000 genomes]
rs8035775	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs8037804	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs8038416	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs8040502	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs8042729	0.91[CEU][hapmap]
rs896796	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9806221	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv1841263	chr15:40902453-40966765	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4924490	INO80	cis	cerebellum	SCAN
rs4924490	RMDN3	cis	Heart Left Ventricle	GTEx
rs4924490	FAM82A2	cis	parietal	SCAN
rs4924490	PLA2G4D	cis	parietal	SCAN
rs4924490	TGFBR3	trans	lymphoblastoid	seeQTL
rs4924490	ZFYVE19	cis	cerebellum	SCAN
rs4924490	RMDN3	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40887800-40961600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:40913800-40986000	Weak transcription	A549	lung
3	chr15:40943000-40971400	Weak transcription	Primary B cells from cord blood	blood
4	chr15:40945000-40984200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:40945200-40961400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:40950000-40981200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:40950200-40964200	Weak transcription	Osteobl	bone
8	chr15:40955200-40964400	Weak transcription	GM12878-XiMat	blood
9	chr15:40955200-40976600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr15:40955200-40983200	Weak transcription	Fetal Intestine Small	intestine
11	chr15:40955800-40976000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:40956800-40963000	Weak transcription	Hela-S3	cervix
13	chr15:40956800-40966000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr15:40956800-40971200	Weak transcription	Dnd41	blood
15	chr15:40957600-40961400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr15:40958400-40966600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr15:40958600-40981000	Weak transcription	Thymus	Thymus
18	chr15:40959000-40961800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:40960400-40977000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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