Variant report

Variant	rs3860228
Chromosome Location	chr3:143145568-143145569
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10513201	0.90[CEU][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs16846341	0.81[CEU][hapmap];0.92[TSI][hapmap]
rs16853522	0.81[CEU][hapmap]
rs16853578	0.90[CEU][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs56078024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770293	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs6782465	0.81[CEU][hapmap];0.92[TSI][hapmap]
rs73144769	0.83[EUR][1000 genomes]
rs73144770	0.83[EUR][1000 genomes]
rs73144771	0.83[EUR][1000 genomes]
rs73144772	0.84[EUR][1000 genomes]
rs73144774	0.84[EUR][1000 genomes]
rs73144777	0.84[EUR][1000 genomes]
rs7374585	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs924576	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv1011088	chr3:143135891-143163169	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3860228	PLSCR4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143139000-143145600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:143140000-143150000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:143142000-143150200	Enhancers	Dnd41	blood
4	chr3:143142800-143145600	Weak transcription	Fetal Thymus	thymus
5	chr3:143143200-143145600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr3:143143200-143145800	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr3:143143200-143146000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:143143200-143146400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:143143200-143161600	Weak transcription	Primary T cells from cord blood	blood
10	chr3:143143600-143146600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr3:143143600-143147600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:143144200-143147000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:143144800-143146800	Weak transcription	Primary B cells from cord blood	blood
14	chr3:143145200-143146400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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