Variant report

Variant	rs948422
Chromosome Location	chr8:61369808-61369809
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10096140	0.89[EUR][1000 genomes]
rs10098769	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10102740	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs10435601	0.92[EUR][1000 genomes]
rs10808709	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10808710	0.93[EUR][1000 genomes]
rs10957133	0.84[EUR][1000 genomes]
rs10957142	0.89[EUR][1000 genomes]
rs10957144	0.89[EUR][1000 genomes]
rs10957145	0.87[EUR][1000 genomes]
rs10957147	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs10957150	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs10957151	0.88[EUR][1000 genomes]
rs1120591	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs11774081	0.91[EUR][1000 genomes]
rs11776939	0.83[EUR][1000 genomes]
rs11777673	0.93[EUR][1000 genomes]
rs11777706	0.91[EUR][1000 genomes]
rs11995549	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11996592	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs12678742	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12680781	0.89[EUR][1000 genomes]
rs12681129	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs1319104	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs1319105	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs13257359	0.89[EUR][1000 genomes]
rs13262390	0.89[EUR][1000 genomes]
rs13265543	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13276831	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13439252	0.87[EUR][1000 genomes]
rs1552071	0.82[EUR][1000 genomes]
rs17814894	0.92[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs1842389	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1893272	0.91[EUR][1000 genomes]
rs1941463	0.91[EUR][1000 genomes]
rs2013112	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2056415	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs2096890	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2155829	0.91[EUR][1000 genomes]
rs2186986	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2272620	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs2272621	0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs2326560	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2326561	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2326562	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs2326568	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2326569	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs2326570	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs2326571	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs2625441	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2625446	0.86[EUR][1000 genomes]
rs28649594	0.92[EUR][1000 genomes]
rs2875967	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs2875968	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs2875973	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs2875974	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs2930040	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs2946154	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs2981277	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs3735825	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3735826	0.88[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs3929643	0.90[EUR][1000 genomes]
rs41420549	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs4403445	0.94[EUR][1000 genomes]
rs4452821	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55825491	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56294255	0.88[EUR][1000 genomes]
rs586377	0.87[EUR][1000 genomes]
rs595255	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs600811	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs603035	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs608401	0.88[EUR][1000 genomes]
rs615031	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs617834	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs625850	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs625979	0.80[JPT][hapmap]
rs629268	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs631408	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6471875	0.85[EUR][1000 genomes]
rs6471885	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6471886	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6471888	0.88[EUR][1000 genomes]
rs652422	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs659118	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs660865	0.85[EUR][1000 genomes]
rs669599	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67420552	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs684066	0.88[EUR][1000 genomes]
rs687978	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6984378	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs6987084	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6992869	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6993019	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6995041	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs6995515	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7000166	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs7001696	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7007434	0.94[EUR][1000 genomes]
rs7012181	0.88[EUR][1000 genomes]
rs7013249	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs7413	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7815543	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs7822169	0.96[EUR][1000 genomes]
rs7824045	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7825612	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7827453	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs7829359	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7830710	0.83[EUR][1000 genomes]
rs7834395	0.95[EUR][1000 genomes]
rs7839474	0.89[EUR][1000 genomes]
rs7839516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7842586	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9298039	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs9643523	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[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	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs948422	RAB2A	cis	Thyroid	GTEx
rs948422	RAB2	cis	normal skin	skin_eQTL
rs948422	RAB2	cis	lesional skin	skin_eQTL
rs948422	RAB2	cis	uninvolved skin	skin_eQTL
rs948422	RAB2A	cis	multi-tissue	Pritchard
rs948422	RAB2A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61368600-61371400	Weak transcription	NHLF	lung
2	chr8:61369200-61370000	Enhancers	Primary B cells from peripheral blood	blood
3	chr8:61369200-61370000	Enhancers	Primary hematopoietic stem cells	blood
4	chr8:61369200-61370000	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr8:61369200-61370600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr8:61369200-61370600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr8:61369400-61375600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr8:61369600-61370600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr8:61369600-61374200	Weak transcription	NHEK	skin
10	chr8:61369600-61379800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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