Variant report

Variant	rs6545558
Chromosome Location	chr2:56436255-56436256
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10210479	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1119821	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs1160647	0.91[CHB][hapmap];0.92[CHD][hapmap]
rs1160648	0.82[CHB][hapmap]
rs12612590	0.82[CHB][hapmap]
rs13026932	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17268667	0.86[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs1861772	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs1990757	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs214047	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2193473	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2193474	0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2193475	0.82[CHB][hapmap]
rs2193476	0.86[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2216323	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2216324	0.81[ASN][1000 genomes]
rs2869526	0.81[YRI][hapmap]
rs2869527	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2869528	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34377123	0.80[ASN][1000 genomes]
rs4672100	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545559	0.91[CHB][hapmap];0.92[CHD][hapmap]
rs6719608	0.91[CEU][hapmap];0.95[CHB][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7579447	0.86[CHB][hapmap];0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs763345	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs888279	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs979504	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs994297	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757799	chr2:56178439-56472394	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2759051	chr2:56178439-56472394	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	nsv874162	chr2:56255832-56480571	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv874169	chr2:56383762-56473480	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6545558	CCDC85A	cis	lymphoblastoid	seeQTL
rs6545558	TSPYL6	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56420600-56443200	Weak transcription	Adipose Nuclei	Adipose
2	chr2:56421200-56437200	Weak transcription	Left Ventricle	heart
3	chr2:56423000-56443400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:56429400-56437200	Strong transcription	HSMM	muscle
5	chr2:56434800-56437800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:56434800-56439200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:56435000-56437400	Weak transcription	HUVEC	blood vessel
8	chr2:56435600-56439600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr2:56435800-56440000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:56436000-56436600	Enhancers	Fetal Brain Male	brain

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