Variant report

Variant	rs955545
Chromosome Location	chr4:76301932-76301933
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10029348	0.85[EUR][1000 genomes]
rs1046662	0.96[CEU][hapmap];0.91[GIH][hapmap];0.85[EUR][1000 genomes]
rs11735018	0.96[CEU][hapmap]
rs11935932	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1351092	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1389443	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1395359	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1395360	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1478174	0.86[EUR][1000 genomes]
rs1564174	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1580297	0.85[EUR][1000 genomes]
rs1600100	0.85[EUR][1000 genomes]
rs1676917	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1817387	0.96[CEU][hapmap]
rs1841932	0.96[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs1841934	0.96[CEU][hapmap]
rs1904103	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2045863	0.92[CEU][hapmap];0.85[GIH][hapmap]
rs2126855	0.86[EUR][1000 genomes]
rs2867920	0.85[EUR][1000 genomes]
rs4593160	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859963	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57749060	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59581284	0.83[EUR][1000 genomes]
rs6833496	0.92[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap]
rs6835579	0.96[CEU][hapmap]
rs6841171	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6841882	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap]
rs7664140	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap]
rs7698352	0.88[CEU][hapmap]
rs786682	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs786684	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs786688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs949611	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010552	chr4:76064415-76325430	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	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
3	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
4	esv2763368	chr4:76190070-76387413	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv461557	chr4:76212995-76363477	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv594688	chr4:76212995-76363477	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	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
8	nsv879493	chr4:76264496-76332975	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv879494	chr4:76264496-76337998	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs955545	THAP6	cis	multi-tissue	Pritchard
rs955545	CCNI	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76301600-76302200	Enhancers	Rectal Mucosa Donor 31	rectum

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