Variant report

Variant	rs10515267
Chromosome Location	chr5:100128202-100128203
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10515265	1.00[ASN][1000 genomes]
rs10515266	1.00[ASN][1000 genomes]
rs1423381	1.00[GIH][hapmap]
rs17159344	1.00[ASN][1000 genomes]
rs17159370	1.00[ASN][1000 genomes]
rs17159464	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17159467	1.00[ASN][1000 genomes]
rs17159519	1.00[ASN][1000 genomes]
rs17159534	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17159602	1.00[ASN][1000 genomes]
rs17159616	1.00[ASN][1000 genomes]
rs17159626	1.00[ASN][1000 genomes]
rs17160732	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17160771	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs17160844	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17779305	1.00[TSI][hapmap]
rs2544911	1.00[GIH][hapmap]
rs2544919	1.00[GIH][hapmap]
rs3776165	1.00[GIH][hapmap]
rs3776166	1.00[GIH][hapmap]
rs3776173	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3857364	1.00[ASN][1000 genomes]
rs6595534	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6878151	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6897681	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73775624	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs768777	1.00[ASN][1000 genomes]
rs7725476	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948969	chr5:99534096-100133827	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1021183	chr5:99625857-100221426	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1017420	chr5:99745775-100133140	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv537825	chr5:99745775-100133140	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1023765	chr5:99915011-100733755	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	esv2762532	chr5:100041758-100136552	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10515267	CXCL10	trans	brain	seeQTL
rs10515267	NAMPT	trans	brain	seeQTL
rs10515267	SOD2	trans	brain	seeQTL
rs10515267	CXCL11	trans	brain	seeQTL
rs10515267	PLSCR1	trans	brain	seeQTL
rs10515267	CXCL2	trans	brain	seeQTL
rs10515267	TXNDC5	trans	brain	seeQTL
rs10515267	LAP3	trans	brain	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100114000-100136400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:100126400-100129200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:100126400-100129200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:100127000-100128600	Weak transcription	Fetal Lung	lung
5	chr5:100127000-100132600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:100127800-100128600	Weak transcription	Dnd41	blood
7	chr5:100128200-100129200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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