Variant report

Variant	rs7017556
Chromosome Location	chr8:61319467-61319468
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10100740	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10101576	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10101714	0.93[EUR][1000 genomes];0.89[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];0.84[MKK][hapmap];0.92[TSI][hapmap]
rs10110436	0.80[EUR][1000 genomes]
rs10504311	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.98[ASN][1000 genomes]
rs10957135	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10957136	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10957137	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10957138	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10957140	0.91[EUR][1000 genomes];0.82[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];0.88[MKK][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10957143	0.80[EUR][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];0.83[MKK][hapmap];0.92[TSI][hapmap]
rs10957149	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11774500	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11775407	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11778529	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11778708	0.81[EUR][1000 genomes];0.82[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]
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];0.82[MKK][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs11782463	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11784284	0.81[EUR][1000 genomes];0.82[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]
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];0.86[MKK][hapmap];0.92[TSI][hapmap]
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];0.88[MKK][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13267828	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13269925	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1480342	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2326556	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28405386	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28542403	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28678079	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2875966	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs34775344	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35837434	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
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];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66983460	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6987523	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6991529	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6993237	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6995397	0.95[CEU][hapmap];0.91[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];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6998294	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7357376	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7812421	0.81[EUR][1000 genomes]
rs7820349	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7822391	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7826226	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7832664	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7832964	0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7842105	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7017556	RAB2	cis	lesional skin	skin_eQTL
rs7017556	RAB2	cis	uninvolved skin	skin_eQTL
rs7017556	LOC643763	cis	parietal	SCAN
rs7017556	RAB2	cis	normal skin	skin_eQTL
rs7017556	RAB2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61309000-61330000	Weak transcription	Right Atrium	heart
2	chr8:61315400-61319800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr8:61317000-61321800	Weak transcription	Fetal Heart	heart
4	chr8:61317800-61320400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr8:61318000-61319800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr8:61318200-61320200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr8:61318600-61320800	Weak transcription	Pancreas	Pancrea
8	chr8:61319000-61321600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr8:61319400-61320600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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