Variant report

Variant	rs2859543
Chromosome Location	chr11:113275579-113275580
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1003641	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1076562	0.92[ASN][1000 genomes]
rs11214598	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11214602	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1124492	0.84[ASN][1000 genomes]
rs1124493	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12224538	0.83[ASN][1000 genomes]
rs1800497	0.86[AFR][1000 genomes]
rs2002453	0.92[ASN][1000 genomes]
rs2005313	0.92[ASN][1000 genomes]
rs2242592	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2245805	0.92[ASN][1000 genomes]
rs2471856	0.88[ASN][1000 genomes]
rs2511521	0.92[ASN][1000 genomes]
rs2587550	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587552	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2734841	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2734842	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2859544	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859545	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4590907	0.83[ASN][1000 genomes]
rs4938014	0.84[ASN][1000 genomes]
rs4938016	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61492892	0.83[ASN][1000 genomes]
rs6275	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6276	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6279	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7122228	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv556444	chr11:113234432-113383394	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1040152	chr11:113258065-113285916	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2859543	TTC12	cis	Heart Left Ventricle	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:113258800-113287400	Weak transcription	Gastric	stomach
2	chr11:113259200-113276000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:113272400-113275800	Weak transcription	Esophagus	oesophagus
4	chr11:113273000-113277600	Weak transcription	Right Ventricle	heart
5	chr11:113274600-113278600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr11:113275200-113275600	Enhancers	Primary hematopoietic stem cells	blood
7	chr11:113275200-113275600	Enhancers	NHEK	skin
8	chr11:113275200-113275800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr11:113275200-113276200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr11:113275200-113277000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr11:113275200-113277200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr11:113275200-113277200	Enhancers	HMEC	breast
13	chr11:113275400-113275600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
14	chr11:113275400-113276800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr11:113275400-113277600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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