Variant report

Variant	rs258763
Chromosome Location	chr5:142652361-142652362
allele	A/T
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]
rs10041520	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10052957	0.88[YRI][hapmap]
rs1866388	0.84[YRI][hapmap]
rs190488	0.89[YRI][hapmap]
rs258747	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs258750	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs258813	0.80[YRI][hapmap];0.87[AFR][1000 genomes]
rs2918416	0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs2918417	0.88[YRI][hapmap]
rs2963149	0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs33383	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs33388	0.88[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4634384	0.87[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6188	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs6191	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6877893	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7716360	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs852975	0.85[AFR][1000 genomes]
rs852976	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852977	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs852980	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs852982	0.88[YRI][hapmap]
rs852983	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853175	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs853180	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs853183	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860457	0.88[YRI][hapmap]
rs864354	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][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	esv1825941	chr5:142568715-142728031	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	esv33748	chr5:142638267-142699595	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs258763	NR3C1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:142642600-142658200	Weak transcription	Osteobl	bone
2	chr5:142643000-142658000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr5:142646600-142672400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr5:142647800-142658800	Weak transcription	Hela-S3	cervix
5	chr5:142648400-142654600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:142648800-142656600	Weak transcription	Primary B cells from cord blood	blood
7	chr5:142649000-142658000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:142649600-142656000	Weak transcription	HSMM	muscle
9	chr5:142650000-142657200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:142650000-142674000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:142650200-142658000	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr5:142650400-142658000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr5:142650600-142677200	Weak transcription	Aorta	Aorta
14	chr5:142650800-142659200	Weak transcription	Thymus	Thymus
15	chr5:142651400-142654800	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr5:142651600-142654600	Weak transcription	A549	lung
17	chr5:142652000-142654600	Weak transcription	GM12878-XiMat	blood
18	chr5:142652000-142655000	Weak transcription	Dnd41	blood
19	chr5:142652200-142669800	Weak transcription	Left Ventricle	heart

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