Variant report

Variant	rs2143004
Chromosome Location	chr20:40715182-40715183
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1126101	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs1126102	0.92[EUR][1000 genomes]
rs1883375	0.95[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs1883380	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2076247	0.92[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs2425467	0.89[EUR][1000 genomes]
rs2425469	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2425470	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2425471	0.94[ASN][1000 genomes]
rs2425472	0.80[CHB][hapmap];0.80[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2425473	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2425475	0.92[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2866942	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2866947	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3091600	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3091875	0.85[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3091889	0.94[ASN][1000 genomes]
rs3091932	0.81[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3092252	0.94[ASN][1000 genomes]
rs3092503	0.94[ASN][1000 genomes]
rs3092588	0.94[ASN][1000 genomes]
rs3092614	0.94[ASN][1000 genomes]
rs6102663	0.81[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs6130027	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7263976	0.90[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs750782	0.88[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][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	nsv3381	chr20:39925326-40765696	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2751913	chr20:40422982-41269321	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv532516	chr20:40451059-41097155	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2143004	YWHAB	cis	cerebellum	SCAN
rs2143004	DHX35	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:40701800-40715200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:40712200-40725800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr20:40714600-40730000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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