Variant report

Variant	rs2884804
Chromosome Location	chr3:54508115-54508116
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11130423	0.85[CEU][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs11707007	0.88[EUR][1000 genomes]
rs11708915	0.91[EUR][1000 genomes]
rs11711518	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs11714447	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.96[EUR][1000 genomes]
rs13073425	0.88[EUR][1000 genomes]
rs13082611	0.83[CHB][hapmap];0.84[CHD][hapmap]
rs13089488	0.88[EUR][1000 genomes]
rs17140	0.96[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs2053862	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[YRI][hapmap]
rs28507696	0.87[EUR][1000 genomes]
rs57828037	0.88[EUR][1000 genomes]
rs58452494	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6414584	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs6445673	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs6445677	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs6445680	0.92[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs6445682	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs6445684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.96[EUR][1000 genomes]
rs6445685	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6445687	1.00[CEU][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs6445690	0.96[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs6772902	0.86[YRI][hapmap]
rs6775352	0.96[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs6789926	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs6790503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs6792203	0.86[YRI][hapmap]
rs6795380	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6798952	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs7372541	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7372624	0.96[EUR][1000 genomes]
rs7372750	0.86[YRI][hapmap]
rs7373217	0.86[CHD][hapmap];0.83[ASN][1000 genomes]
rs7373390	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs7373932	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7374204	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7428361	0.90[EUR][1000 genomes]
rs7431090	0.95[EUR][1000 genomes]
rs7432845	0.96[CEU][hapmap]
rs7636708	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.96[EUR][1000 genomes]
rs9816842	0.87[EUR][1000 genomes]
rs9855891	0.91[CHB][hapmap];0.98[CHD][hapmap];0.82[JPT][hapmap]
rs9874147	0.88[EUR][1000 genomes]
rs9874177	0.96[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs9879189	0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv817210	chr3:54365684-54511164	Enhancers Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1010348	chr3:54435563-54508115	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv998970	chr3:54455794-54516789	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv876810	chr3:54480798-54585416	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2884804	KCTD6	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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