Variant report

Variant	rs4744610
Chromosome Location	chr9:73361373-73361374
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10115414	0.88[ASN][1000 genomes]
rs10120897	0.87[ASN][1000 genomes]
rs10123720	0.88[ASN][1000 genomes]
rs10123776	0.88[ASN][1000 genomes]
rs10124691	0.88[ASN][1000 genomes]
rs10124821	0.88[ASN][1000 genomes]
rs10868882	0.80[ASN][1000 genomes]
rs10868885	0.87[CHB][hapmap]
rs11142563	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11142583	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1160741	0.86[ASN][1000 genomes]
rs1160742	0.88[ASN][1000 genomes]
rs1328143	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1328148	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4744611	0.85[AFR][1000 genomes]
rs4744612	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4745025	0.87[ASN][1000 genomes]
rs4745026	0.87[ASN][1000 genomes]
rs58302882	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60864427	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6560150	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7025697	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7031754	0.87[ASN][1000 genomes]
rs7032467	0.88[ASN][1000 genomes]
rs7036878	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7045063	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7048348	0.88[ASN][1000 genomes]
rs7848308	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7875629	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893440	chr9:73225802-73434585	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	76 gene(s)	inside rSNPs	diseases
2	nsv6556	chr9:73304158-73363098	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv969739	chr9:73318954-73369474	Strong transcription Enhancers Weak transcription ZNF genes & repeats	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4744610	TJP2	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:73352800-73367600	Weak transcription	Fetal Kidney	kidney
2	chr9:73356000-73364800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr9:73356600-73368800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:73356800-73376000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr9:73357800-73362600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:73358600-73365400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:73361000-73362800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:73361000-73362800	Enhancers	NHDF-Ad	bronchial
9	chr9:73361000-73363000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr9:73361200-73362600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:73361200-73362800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:73361200-73364200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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