Variant report

Variant	rs2569956
Chromosome Location	chr3:144157149-144157150
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs2249820	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2569944	0.91[ASN][1000 genomes]
rs2569945	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2569948	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2569949	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2569950	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2569951	0.92[ASN][1000 genomes]
rs2569953	0.82[ASN][1000 genomes]
rs2569954	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2569955	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2717372	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2717373	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2717374	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2717399	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2717400	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2717401	0.81[CEU][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6440252	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6771442	0.90[ASN][1000 genomes]
rs6803756	0.90[ASN][1000 genomes]
rs9818367	0.90[ASN][1000 genomes]

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	nsv532633	chr3:143802417-144440646	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1011685	chr3:143959237-144218424	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv536751	chr3:143959237-144218424	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv591928	chr3:144050897-144822081	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv591929	chr3:144123401-144188561	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv1012058	chr3:144139713-144183108	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv536752	chr3:144151900-144183108	Enhancers ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv591930	chr3:144152222-144180576	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2569956	TM4SF18	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:144156800-144157200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:144156800-144157200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:144156800-144157400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:144157000-144158200	ZNF genes & repeats	GM12878-XiMat	blood

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