Variant report

Variant	rs1552071
Chromosome Location	chr8:61306938-61306939
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	chr8:61304106..61306671-chr8:61306892..61309869,2	K562	blood:
2	chr8:61181201..61184970-chr8:61306411..61309605,3	K562	blood:

Extended variants
information (count: 85 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10096140	0.82[EUR][1000 genomes]
rs10098769	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs10102740	0.96[CEU][hapmap]
rs10808709	0.92[CEU][hapmap]
rs10957133	0.89[EUR][1000 genomes]
rs10957142	0.83[EUR][1000 genomes]
rs10957144	0.82[EUR][1000 genomes]
rs10957147	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10957151	0.82[EUR][1000 genomes]
rs11776939	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11995549	0.81[EUR][1000 genomes]
rs11996592	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12681129	0.81[EUR][1000 genomes]
rs1319104	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1319105	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs13257359	0.83[EUR][1000 genomes]
rs13262390	0.82[EUR][1000 genomes]
rs13265543	0.82[EUR][1000 genomes]
rs13439252	0.81[EUR][1000 genomes]
rs17814894	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1842389	0.89[EUR][1000 genomes]
rs1893272	0.85[EUR][1000 genomes]
rs1941463	0.84[EUR][1000 genomes]
rs2013112	0.81[EUR][1000 genomes]
rs2056415	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs2096890	0.81[EUR][1000 genomes]
rs2155829	0.85[EUR][1000 genomes]
rs2186986	0.81[EUR][1000 genomes]
rs2272620	1.00[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs2272621	0.83[EUR][1000 genomes]
rs2326560	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs2326561	0.96[CEU][hapmap]
rs2326562	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs2326568	0.96[CEU][hapmap]
rs2326569	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs2326570	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs2326571	0.96[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2875967	0.96[CEU][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs2875968	0.96[CEU][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs2875973	0.96[CEU][hapmap]
rs2875974	0.96[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs2930040	0.82[EUR][1000 genomes]
rs2946154	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs2981277	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs3735825	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs3735826	0.96[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs41420549	0.96[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs56294255	0.82[EUR][1000 genomes]
rs586377	0.81[EUR][1000 genomes]
rs595255	0.82[EUR][1000 genomes]
rs608401	0.82[EUR][1000 genomes]
rs617834	0.81[EUR][1000 genomes]
rs6471875	0.90[EUR][1000 genomes]
rs6471885	0.81[EUR][1000 genomes]
rs6471886	0.81[EUR][1000 genomes]
rs6471888	0.82[EUR][1000 genomes]
rs67420552	0.80[EUR][1000 genomes]
rs684066	0.82[EUR][1000 genomes]
rs6984378	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6987084	0.96[CEU][hapmap]
rs6992869	0.85[EUR][1000 genomes]
rs6995041	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs7000166	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs7001696	0.82[EUR][1000 genomes]
rs7012181	0.81[EUR][1000 genomes]
rs7013249	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs7815543	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs7822169	0.81[EUR][1000 genomes]
rs7824045	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs7825612	0.89[EUR][1000 genomes]
rs7827453	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs7829359	0.96[CEU][hapmap]
rs7830710	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7834395	0.80[EUR][1000 genomes]
rs7839474	0.83[EUR][1000 genomes]
rs7839516	0.92[CEU][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs7842586	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs9298039	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs948422	0.82[EUR][1000 genomes]
rs9643523	0.96[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1022752	chr8:61095248-61322302	Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	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
4	nsv831334	chr8:61148796-61330190	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv890944	chr8:61252500-61307115	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1552071	RAB2A	cis	multi-tissue	Pritchard
rs1552071	RAB2	cis	lesional skin	skin_eQTL
rs1552071	RAB2A	Cis_1M	lymphoblastoid	RTeQTL
rs1552071	RAB2	cis	uninvolved skin	skin_eQTL
rs1552071	RAB2A	cis	lymphoblastoid	seeQTL
rs1552071	RAB2A	cis	Thyroid	GTEx
rs1552071	RAB2	cis	multi-tissue	Pritchard
rs1552071	RAB2	cis	normal skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61302400-61308800	Weak transcription	Brain Hippocampus Middle	brain
2	chr8:61304800-61308600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr8:61305000-61308600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr8:61305800-61310000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr8:61306200-61307000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr8:61306600-61307000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr8:61306600-61308000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr8:61306600-61308800	Weak transcription	Fetal Lung	lung
9	chr8:61306800-61308400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr8:61306800-61308600	Weak transcription	Fetal Stomach	stomach

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