Variant report

Variant	rs6471880
Chromosome Location	chr8:61373340-61373341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10087760	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10092773	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10102945	0.86[ASN][1000 genomes]
rs10504312	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11984591	0.95[LWK][hapmap];0.92[YRI][hapmap]
rs11988766	0.85[ASN][1000 genomes]
rs11988798	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11997369	0.95[LWK][hapmap];0.92[YRI][hapmap]
rs12548711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1318227	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1552070	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1842388	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1893277	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1893279	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1941467	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2012856	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2068587	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2155831	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6471873	0.90[JPT][hapmap]
rs6471877	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6471881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6982032	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6982404	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6986664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6993588	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6994192	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6998307	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6999822	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7001436	0.94[JPT][hapmap]
rs7004236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7814226	0.86[ASN][1000 genomes]
rs7819947	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7824474	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7824671	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7828383	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7831106	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7841648	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9785091	0.91[EUR][1000 genomes];0.98[ASN][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	nsv917756	chr8:60942299-61862796	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv971314	chr8:61359401-61436209	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6471880	RP11-163N6.2	cis	Thyroid	GTEx
rs6471880	RAB2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61369400-61375600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr8:61369600-61374200	Weak transcription	NHEK	skin
3	chr8:61369600-61379800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:61370600-61379800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr8:61371600-61375400	Enhancers	Fetal Brain Male	brain
6	chr8:61372000-61375200	Weak transcription	Fetal Lung	lung
7	chr8:61373000-61373800	Weak transcription	Fetal Brain Female	brain

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