Variant report

Variant	rs963885
Chromosome Location	chr3:143037982-143037983
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:143030582..143033668-chr3:143037304..143039802,3	K562	blood:
2	chr3:142943499..142945080-chr3:143037580..143040276,2	K562	blood:
3	chr3:143028279..143030490-chr3:143036319..143039500,3	K562	blood:
4	chr3:143035923..143038804-chr3:143039604..143041448,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240888	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10804689	0.83[CHB][hapmap]
rs10804690	0.83[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10935488	0.88[CEU][hapmap];0.92[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10935489	0.85[CHD][hapmap]
rs11915857	0.83[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs12494318	0.93[EUR][1000 genomes]
rs12497617	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12633063	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066661	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13067348	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1501628	0.83[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1501629	0.83[CHB][hapmap];0.82[CHD][hapmap];0.86[TSI][hapmap]
rs1550547	0.88[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16853428	0.83[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs16853431	0.80[ASN][1000 genomes]
rs1837784	0.83[CHB][hapmap]
rs2165518	0.83[CHB][hapmap];0.85[CHD][hapmap];0.86[TSI][hapmap]
rs2352725	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs2883015	0.83[CHB][hapmap];0.85[CHD][hapmap];0.86[TSI][hapmap];0.80[ASN][1000 genomes]
rs6440163	0.83[CHB][hapmap]
rs6440164	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]
rs6768217	0.83[CHB][hapmap];0.80[ASN][1000 genomes]
rs6769555	0.83[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6770495	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6806677	0.83[CHB][hapmap]
rs729509	0.80[ASN][1000 genomes]
rs729511	0.85[CHD][hapmap];0.86[TSI][hapmap];0.80[ASN][1000 genomes]
rs7632299	0.88[CHD][hapmap]
rs9332458	0.88[CHD][hapmap]
rs968586	0.83[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs968587	0.88[CHD][hapmap];0.81[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
rs963885	PLSCR4	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143015200-143039600	Weak transcription	Brain Substantia Nigra	brain
2	chr3:143018400-143039400	Weak transcription	Primary B cells from cord blood	blood
3	chr3:143022400-143048200	Weak transcription	Psoas Muscle	Psoas
4	chr3:143025600-143040000	Weak transcription	Right Atrium	heart
5	chr3:143026600-143047400	Weak transcription	Spleen	Spleen
6	chr3:143029400-143045800	Weak transcription	Adipose Nuclei	Adipose
7	chr3:143029800-143045200	Weak transcription	Primary T cells from cord blood	blood
8	chr3:143033800-143048400	Weak transcription	Fetal Stomach	stomach
9	chr3:143034400-143047400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:143034400-143048600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:143035000-143038200	Weak transcription	K562	blood
12	chr3:143035000-143042800	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr3:143037000-143038200	Enhancers	Fetal Lung	lung
14	chr3:143037800-143045800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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