Variant report

Variant	rs2621462
Chromosome Location	chr4:96247498-96247499
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11937484	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1351772	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1542616	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1843018	1.00[CEU][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2170780	0.89[LWK][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs2621439	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2621463	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2626050	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2626051	1.00[CEU][hapmap];0.92[GIH][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2626057	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2626062	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2626063	1.00[CEU][hapmap];0.92[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2626069	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4699419	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56184934	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56219612	0.83[EUR][1000 genomes]
rs56663807	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56916207	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58809210	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59179643	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61076479	0.85[EUR][1000 genomes]
rs61570927	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62307079	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6532550	1.00[CEU][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6846883	0.83[EUR][1000 genomes]
rs6856212	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72659904	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7436599	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7440986	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7441683	1.00[AMR][1000 genomes];0.97[EUR][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	nsv869528	chr4:95537649-96368018	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1001955	chr4:96216118-96445841	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv471768	chr4:96246500-96247595	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
4	nsv594911	chr4:96246506-96247498	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
5	esv2763844	chr4:96246506-96255197	Weak transcription Enhancers Strong transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
6	esv20571	chr4:96246527-96247542	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
7	nsv594913	chr4:96246746-96247498	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
8	nsv594914	chr4:96246802-96247498	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2621462	PDLIM5	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:96223000-96252400	Weak transcription	Fetal Lung	lung
2	chr4:96239600-96250000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:96239600-96284400	Weak transcription	Aorta	Aorta
4	chr4:96240600-96248200	Weak transcription	Brain Anterior Caudate	brain
5	chr4:96241000-96260800	Weak transcription	Brain Substantia Nigra	brain
6	chr4:96241000-96267600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr4:96242000-96260200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr4:96243000-96259600	Weak transcription	Brain Hippocampus Middle	brain
9	chr4:96243400-96263200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr4:96246200-96255000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:96246800-96247600	Enhancers	Brain Angular Gyrus	brain
12	chr4:96247200-96247600	Enhancers	HUVEC	blood vessel
13	chr4:96247200-96265000	Weak transcription	Brain Cingulate Gyrus	brain

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