Variant report

Variant	rs10935489
Chromosome Location	chr3:143057833-143057834
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:143055149..143058729-chr3:143058882..143061743,3	K562	blood:
2	chr3:143057632..143059854-chr3:143064608..143066559,2	K562	blood:
3	chr3:143049101..143052451-chr3:143056626..143059965,3	K562	blood:

Variant related genes	Relation type
ENSG00000240012	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10446325	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10804689	0.92[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs10804690	0.92[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs10804691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935488	0.84[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs11915857	0.92[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12493355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12633063	0.85[CHD][hapmap]
rs1393071	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1501628	0.92[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs1501629	0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs1550547	0.84[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs16853428	0.92[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16853431	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17637467	0.82[TSI][hapmap]
rs1837784	0.92[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2165518	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2352725	0.92[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs2883015	0.92[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs6440163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6440164	0.92[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6768217	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6769555	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs6806677	0.92[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs729509	0.96[ASN][1000 genomes]
rs729511	0.84[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7632299	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7652901	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9332458	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs963885	0.85[CHD][hapmap]
rs968586	0.92[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs968587	0.84[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.95[ASN][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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv2757894	chr3:142992697-143285979	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2759184	chr3:142992697-143285979	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10935489	ACAP3	trans	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143049200-143061200	Weak transcription	Fetal Thymus	thymus
2	chr3:143052600-143061600	Weak transcription	Dnd41	blood
3	chr3:143056800-143058000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:143056800-143058000	Weak transcription	Placenta	Placenta
5	chr3:143056800-143058800	Enhancers	Fetal Lung	lung
6	chr3:143056800-143062400	Weak transcription	Primary T cells from cord blood	blood
7	chr3:143057400-143058800	Weak transcription	Fetal Kidney	kidney

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