Variant report

Variant	rs2326556
Chromosome Location	chr8:61335494-61335495
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:61335203-61335659	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000255840	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10091703	0.81[EUR][1000 genomes]
rs10100740	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs10101576	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10101714	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10109278	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap]
rs10110436	0.81[EUR][1000 genomes]
rs10504311	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.96[ASN][1000 genomes]
rs10957135	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10957136	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10957137	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10957138	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10957140	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10957141	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10957143	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10957146	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs10957149	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11774500	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11775407	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11778529	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11778708	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11778772	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11778888	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11782178	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.80[MKK][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11782463	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11784284	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11786146	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11988528	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs12678694	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs12681841	0.80[EUR][1000 genomes]
rs13266707	0.94[ASW][hapmap];0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13267828	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13269925	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1480342	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2326557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28405386	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28495747	0.80[EUR][1000 genomes]
rs28542403	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28678079	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2875966	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs34523017	0.80[EUR][1000 genomes]
rs34775344	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35837434	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35853087	0.80[EUR][1000 genomes]
rs602724	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs603239	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs610455	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap]
rs6471883	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6471884	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs649634	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap]
rs66983460	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs671275	0.95[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs684573	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap]
rs6987523	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6991529	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6993237	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs6995397	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs6996344	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6998294	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7017556	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7357376	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs7812421	0.83[EUR][1000 genomes]
rs7820349	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7822391	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7826226	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7832664	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7832964	0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7842105	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9437	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap]
rs9643524	0.80[EUR][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	esv3371465	chr8:61115030-61356658	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2326556	RAB2	cis	multi-tissue	Pritchard
rs2326556	RAB2	cis	uninvolved skin	skin_eQTL
rs2326556	LOC643763	cis	parietal	SCAN
rs2326556	RAB2	cis	normal skin	skin_eQTL
rs2326556	RAB2A	Cis_1M	lymphoblastoid	RTeQTL
rs2326556	RAB2	cis	lesional skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61334600-61336000	Enhancers	Placenta	Placenta

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