Variant report

Variant	rs6440164
Chromosome Location	chr3:143052348-143052349
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:143051394..143054919-chr3:143057283..143061130,3	K562	blood:
2	chr3:143046217..143048916-chr3:143050759..143052463,2	K562	blood:
3	chr3:143049101..143052451-chr3:143056626..143059965,3	K562	blood:

Variant related genes	Relation type
ENSG00000240012	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10446325	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs10804689	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10804690	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10804691	0.91[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs10935488	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10935489	0.92[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs11915857	0.83[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs12493355	0.92[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs12494318	0.84[EUR][1000 genomes]
rs12497617	0.84[EUR][1000 genomes]
rs12633063	0.85[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13066661	0.82[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13067348	0.82[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1393071	0.92[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs1501628	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1501629	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1550547	0.85[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16853428	0.83[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs16853431	0.95[ASN][1000 genomes]
rs1837784	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2165518	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2352725	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2883015	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6440163	0.91[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs6768217	0.83[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6769555	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6770495	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6806677	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs729509	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs729511	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7632299	0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7652901	0.81[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs9332458	0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs963885	0.83[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs968586	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968587	0.92[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.95[MKK][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[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
rs6440164	PLSCR4	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143046600-143056200	Weak transcription	Primary T cells from cord blood	blood
2	chr3:143049200-143053000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:143049200-143056200	Weak transcription	HSMMtube	muscle
4	chr3:143049200-143056400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:143049200-143061200	Weak transcription	Fetal Thymus	thymus
6	chr3:143050200-143056200	Weak transcription	Ovary	ovary
7	chr3:143050600-143054200	Weak transcription	Fetal Lung	lung
8	chr3:143050800-143052400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:143051200-143056200	Weak transcription	NHDF-Ad	bronchial
10	chr3:143051600-143052400	Enhancers	Fetal Brain Female	brain
11	chr3:143051800-143052600	Enhancers	Dnd41	blood
12	chr3:143052200-143052600	Enhancers	Fetal Brain Male	brain

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