Variant report

Variant	rs12421345
Chromosome Location	chr11:104706319-104706320
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10895735	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10895740	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10895742	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11226520	0.80[AMR][1000 genomes]
rs11226540	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11226546	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs11226547	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs11226550	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs11605849	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11825902	0.83[CHB][hapmap]
rs12418917	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12422201	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs17103153	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2005513	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs478650	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs491011	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs491945	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs528641	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs532705	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs548968	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs549691	0.86[JPT][hapmap]
rs561999	0.87[ASN][1000 genomes]
rs573894	0.90[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs579156	0.81[CHB][hapmap]
rs595395	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs626771	0.86[JPT][hapmap]
rs641046	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs656251	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs693312	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046098	chr11:104207210-105003661	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1054456	chr11:104358924-104805251	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv531430	chr11:104380924-105194452	Genic enhancers Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv826072	chr11:104662708-104768357	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv832255	chr11:104674918-104846961	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12421345	CASP1///COP1	Cis_1M	lymphoblastoid	RTeQTL
rs12421345	CASP4	Cis_1M	lymphoblastoid	RTeQTL
rs12421345	CASP1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:104691600-104707600	Weak transcription	Fetal Brain Male	brain

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