Variant report

Variant	rs1542233
Chromosome Location	chr3:118995683-118995684
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:118994260..118996031-chr3:119041098..119043621,2	MCF-7	breast:
2	chr3:118994969..118996823-chr3:119062476..119065328,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241155	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10934489	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11914541	0.88[AMR][1000 genomes]
rs11918598	0.80[MEX][hapmap]
rs2594727	0.82[AMR][1000 genomes]
rs2717266	0.84[AMR][1000 genomes]
rs2971544	0.82[AMR][1000 genomes]
rs4687993	0.83[ASW][hapmap];0.91[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4687994	0.80[YRI][hapmap]
rs56269733	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6438517	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6775982	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6800491	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7620780	0.86[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes]
rs7622994	0.86[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes]
rs7625392	0.92[MEX][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes]
rs7649558	0.88[AMR][1000 genomes]
rs9812615	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9822038	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9827972	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9834125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851458	0.81[EUR][1000 genomes];0.98[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv18354	chr3:118855337-119000251	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1542233	CD86	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118994200-118995800	Enhancers	Primary T cells from cord blood	blood
2	chr3:118994400-118995800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:118994400-118995800	Enhancers	Left Ventricle	heart
4	chr3:118994400-118996400	Enhancers	Lung	lung
5	chr3:118994600-118996400	Enhancers	Placenta	Placenta
6	chr3:118994800-118997800	Weak transcription	Fetal Heart	heart
7	chr3:118994800-118998000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:118994800-118998000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:118995000-118997000	Weak transcription	Right Atrium	heart
10	chr3:118995000-118997800	Weak transcription	A549	lung
11	chr3:118995200-118997600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:118995600-118995800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:118995600-118996000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:118995600-118997600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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