Variant report

Variant	rs2572417
Chromosome Location	chr8:11111462-11111463
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10098488	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs10481445	0.82[EUR][1000 genomes]
rs10503418	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs11250127	0.84[CEU][hapmap]
rs1347409	0.84[ASN][1000 genomes]
rs1347410	1.00[CEU][hapmap];0.83[JPT][hapmap];0.92[EUR][1000 genomes]
rs1435278	0.82[EUR][1000 genomes]
rs17797443	0.84[CEU][hapmap]
rs1865518	0.87[ASN][1000 genomes]
rs1897950	0.84[CEU][hapmap]
rs2060465	0.84[CEU][hapmap]
rs2099456	0.84[CEU][hapmap]
rs2164272	0.84[CEU][hapmap]
rs2164273	0.84[CEU][hapmap]
rs2293855	0.81[CEU][hapmap]
rs2293856	0.81[CEU][hapmap]
rs2572408	0.84[EUR][1000 genomes]
rs2572418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2572422	0.85[ASN][1000 genomes]
rs2572431	0.84[EUR][1000 genomes]
rs2736277	0.80[CEU][hapmap]
rs2736375	0.89[EUR][1000 genomes]
rs3808509	0.84[CEU][hapmap]
rs3808513	0.84[CEU][hapmap]
rs4504596	0.82[CHB][hapmap];0.93[CHD][hapmap];0.87[ASN][1000 genomes]
rs4568582	0.84[CEU][hapmap]
rs6601578	0.81[CEU][hapmap]
rs6985146	0.84[CEU][hapmap]
rs6985460	0.84[CEU][hapmap]
rs6991606	0.84[CEU][hapmap]
rs765731	0.83[EUR][1000 genomes]
rs920051	0.87[ASN][1000 genomes]
rs920053	0.88[CHB][hapmap];0.87[ASN][1000 genomes]
rs9286062	0.87[GIH][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv1815171	chr8:10940039-11128712	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv831233	chr8:11046854-11234384	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1022525	chr8:11066191-11309356	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv539474	chr8:11066191-11309356	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2572417	TDH	cis	parietal	SCAN
rs2572417	DEFB134	cis	cerebellum	SCAN
rs2572417	NEIL2	cis	Nerve Tibial	GTEx
rs2572417	C8orf79	cis	parietal	SCAN
rs2572417	THEX1	Cis_chr	lymphoblastoid	RTeQTL
rs2572417	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs2572417	C8orf13	cis	multi-tissue	Pritchard
rs2572417	CLDN23	cis	multi-tissue	Pritchard
rs2572417	PRSS55	cis	cerebellum	SCAN
rs2572417	C8orf48	cis	cerebellum	SCAN
rs2572417	BLK	Cis_1M	lymphoblastoid	RTeQTL
rs2572417	FLJ10661	cis	cerebellum	SCAN
rs2572417	CTSB	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11101200-11116000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:11110400-11112000	Enhancers	Colon Smooth Muscle	Colon
3	chr8:11111400-11111600	Enhancers	Primary B cells from peripheral blood	blood

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