Variant report

Variant	rs10890845
Chromosome Location	chr11:108334321-108334322
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr11:108334279-108334364	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:108333493..108335772-chr11:108366230..108368651,2	MCF-7	breast:
2	chr11:108332946..108340923-chr11:108359972..108371658,26	K562	blood:
3	chr11:108333954..108342521-chr11:108361561..108373383,35	K562	blood:
4	chr11:108333831..108335607-chr11:108336969..108339271,2	MCF-7	breast:

Variant related genes	Relation type
C11orf65	TF binding region
ENSG00000178202	Chromatin interaction
ENSG00000166323	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10890837	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10890838	1.00[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10890844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890846	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11212650	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11212653	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11212674	0.89[EUR][1000 genomes]
rs11825355	1.00[JPT][hapmap]
rs11828864	0.85[EUR][1000 genomes]
rs12274479	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12278954	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17107969	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs17107980	1.00[JPT][hapmap]
rs17108024	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17108054	0.83[CHD][hapmap]
rs1801516	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs2234994	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs3092836	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs3092856	1.00[JPT][hapmap]
rs3092991	1.00[CEU][hapmap]
rs3092993	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs4753840	1.00[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes]
rs4753843	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4754317	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs4988023	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs4988050	1.00[JPT][hapmap]
rs4988131	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs55930851	0.96[EUR][1000 genomes]
rs7115351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7131306	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap]
rs72992163	0.89[EUR][1000 genomes]
rs72992175	0.96[EUR][1000 genomes]
rs72992191	0.90[EUR][1000 genomes]
rs72993806	0.85[EUR][1000 genomes]
rs72997833	0.85[EUR][1000 genomes]
rs7396719	0.85[EUR][1000 genomes]
rs7931985	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs7938612	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7947933	0.85[EUR][1000 genomes]

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	nsv1052254	chr11:108122683-108845008	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv541164	chr11:108122683-108845008	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv832263	chr11:108183372-108384391	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10890845	ATM,NPAT	cis	brain	BrainEAC
rs10890845	CUL5	cis	multi-tissue	Pritchard
rs10890845	NPAT	cis	cerebellum	SCAN
rs10890845	NPAT	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108333400-108336200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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