Variant report

Variant	rs1550547
Chromosome Location	chr3:143040746-143040747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:143035923..143038804-chr3:143039604..143041448,2	MCF-7	breast:
2	chr3:143039326..143043088-chr3:143044192..143047844,4	K562	blood:
3	chr3:142839410..142843770-chr3:143040182..143043401,3	K562	blood:
4	chr3:142840859..142843770-chr3:143040182..143042870,2	K562	blood:

Variant related genes	Relation type
ENSG00000241679	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	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs10804689	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10804690	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10804691	0.83[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs10935488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10935489	0.84[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs11915857	0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs12493355	0.84[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs12494318	0.88[EUR][1000 genomes]
rs12497617	0.89[EUR][1000 genomes]
rs12633063	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13066661	0.96[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13067348	0.96[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1393071	0.84[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1501628	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1501629	0.92[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.92[ASN][1000 genomes]
rs16853428	0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs16853431	0.93[ASN][1000 genomes]
rs1837784	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2165518	0.92[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.92[ASN][1000 genomes]
rs2352725	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2883015	0.92[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.93[ASN][1000 genomes]
rs6440163	0.83[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6440164	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]
rs6768217	0.92[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs6769555	0.81[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6770495	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6806677	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs729509	0.93[ASN][1000 genomes]
rs729511	0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.93[ASN][1000 genomes]
rs7632299	0.84[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs7652901	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs9332458	0.84[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs963885	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]
rs968586	0.81[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs968587	0.84[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.94[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
rs1550547	PLSCR4	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143022400-143048200	Weak transcription	Psoas Muscle	Psoas
2	chr3:143026600-143047400	Weak transcription	Spleen	Spleen
3	chr3:143029400-143045800	Weak transcription	Adipose Nuclei	Adipose
4	chr3:143029800-143045200	Weak transcription	Primary T cells from cord blood	blood
5	chr3:143033800-143048400	Weak transcription	Fetal Stomach	stomach
6	chr3:143034400-143047400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:143034400-143048600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:143035000-143042800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr3:143037800-143045800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr3:143038200-143045600	Weak transcription	Fetal Lung	lung
11	chr3:143038800-143041400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:143039200-143045200	Weak transcription	Fetal Thymus	thymus
13	chr3:143039400-143040800	Enhancers	Primary B cells from cord blood	blood
14	chr3:143040400-143042000	Weak transcription	K562	blood
15	chr3:143040400-143045200	Weak transcription	Primary B cells from peripheral blood	blood

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