Variant report

Variant	rs1478174
Chromosome Location	chr4:76393189-76393190
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10029348	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10031553	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10034359	1.00[YRI][hapmap]
rs1046662	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11728327	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11729286	1.00[YRI][hapmap]
rs11730978	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11735018	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11935932	0.92[EUR][1000 genomes]
rs13112378	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13119499	1.00[YRI][hapmap]
rs13136001	1.00[YRI][hapmap]
rs13145288	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1351092	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1389443	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1395359	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs1395360	0.83[EUR][1000 genomes]
rs1564174	0.94[EUR][1000 genomes]
rs1580297	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1600100	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1676917	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1817387	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1841932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1841934	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2045863	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2126855	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28507535	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2867920	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2867921	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4593160	0.86[EUR][1000 genomes]
rs4859963	0.87[EUR][1000 genomes]
rs57749060	0.81[EUR][1000 genomes]
rs59581284	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6535523	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6815241	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6816603	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6823674	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6829753	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6833496	0.96[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6835579	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6841171	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6841882	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7661659	1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7664140	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7698352	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs786682	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs786684	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs786688	0.96[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap]
rs9041	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs949611	0.86[EUR][1000 genomes]
rs955545	0.86[EUR][1000 genomes]
rs9998529	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594687	chr4:76154064-76502748	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv998511	chr4:76184807-76398377	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv534570	chr4:76214619-76498362	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1478174	THAP6	cis	multi-tissue	Pritchard
rs1478174	CCNI	cis	cerebellum	SCAN
rs1478174	THAP6	cis	lymphoblastoid	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76391800-76396800	Weak transcription	HSMM	muscle
2	chr4:76392000-76395400	Weak transcription	Primary T cells from cord blood	blood
3	chr4:76392000-76396200	Weak transcription	Primary B cells from cord blood	blood
4	chr4:76392000-76402400	Weak transcription	Liver	Liver
5	chr4:76392600-76434800	Weak transcription	Gastric	stomach
6	chr4:76392800-76403000	Weak transcription	Fetal Brain Female	brain

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