Variant report

Variant	rs6549261
Chromosome Location	chr3:70039845-70039846
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:70038710..70041426-chr3:70048792..70051266,2	K562	blood:
2	chr3:70037680..70040210-chr3:70047402..70050292,3	K562	blood:

Variant related genes	Relation type
ENSG00000240405	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1021413	0.95[CHB][hapmap]
rs1027233	0.81[AMR][1000 genomes]
rs1157456	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11923682	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11926368	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12495230	0.92[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.80[JPT][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1388649	0.83[AMR][1000 genomes]
rs1491686	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1491695	0.92[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs1491698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1492055	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1492056	0.81[AMR][1000 genomes]
rs1546075	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17727959	0.84[ASN][1000 genomes]
rs1873583	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1873584	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1907647	0.83[ASN][1000 genomes]
rs2131122	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2172211	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs28524674	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34790356	0.81[ASN][1000 genomes]
rs35180789	0.85[ASN][1000 genomes]
rs3821364	1.00[CHB][hapmap]
rs3967688	0.83[ASN][1000 genomes]
rs4855453	0.95[CHB][hapmap]
rs4855454	0.95[CHB][hapmap]
rs4855455	0.95[CHB][hapmap]
rs56351003	0.85[ASN][1000 genomes]
rs576	0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6549255	0.85[ASN][1000 genomes]
rs6549257	0.80[ASN][1000 genomes]
rs6549258	0.80[ASN][1000 genomes]
rs6549259	0.80[ASN][1000 genomes]
rs6549260	0.83[ASN][1000 genomes]
rs6549262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6549264	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6549265	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6549266	0.84[AMR][1000 genomes]
rs6772684	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6784666	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809508	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs704246	0.95[CHB][hapmap];0.83[CHD][hapmap]
rs7431913	0.80[ASN][1000 genomes]
rs7634340	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7634564	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7647661	0.84[AMR][1000 genomes]
rs902711	0.85[ASN][1000 genomes]
rs902712	0.85[ASN][1000 genomes]
rs923702	0.80[ASN][1000 genomes]
rs9310178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9310179	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310180	0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs956436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9809122	0.80[AMR][1000 genomes]
rs9815287	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9834141	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9839734	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9840397	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9840590	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9849031	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851891	0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9863457	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868203	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533396	chr3:69964029-70538306	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6549261	RP11-460N16.1	cis	Artery Aorta	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:70037400-70040800	Weak transcription	Aorta	Aorta
2	chr3:70037600-70045200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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