Variant report

Variant	rs9870579
Chromosome Location	chr3:139679616-139679617
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	chr3:139673841..139676667-chr3:139679363..139682238,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10935363	0.85[CEU][hapmap]
rs11927306	0.85[CEU][hapmap]
rs11927384	0.85[CEU][hapmap]
rs1365152	0.81[GIH][hapmap]
rs2114167	0.81[GIH][hapmap]
rs2350274	0.81[GIH][hapmap]
rs28698664	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35018094	0.82[EUR][1000 genomes]
rs6439886	0.85[CEU][hapmap]
rs6806737	0.85[CEU][hapmap]
rs7356017	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7615793	0.81[GIH][hapmap]
rs7617850	0.91[CEU][hapmap]
rs7637853	0.85[CEU][hapmap]
rs9810814	0.82[CEU][hapmap]
rs9813092	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9813297	0.81[GIH][hapmap]
rs9821561	0.85[CEU][hapmap]
rs9821898	0.82[EUR][1000 genomes]
rs9824300	0.82[EUR][1000 genomes]
rs9824570	0.81[GIH][hapmap]
rs9824931	1.00[GIH][hapmap]
rs9835329	1.00[GIH][hapmap];0.80[EUR][1000 genomes]
rs9852679	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9859388	0.85[CEU][hapmap]
rs9860322	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9864420	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9870376	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9870392	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv998423	chr3:139526446-139947336	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv877544	chr3:139642572-139688415	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv460866	chr3:139661938-139704174	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv591859	chr3:139661938-139704174	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv829738	chr3:139670836-139851945	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9870579	TFDP2	cis	parietal	SCAN
rs9870579	SLC25A36	cis	cerebellum	SCAN
rs9870579	ESYT3	cis	cerebellum	SCAN
rs9870579	MRAS	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139668200-139698800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:139669200-139682200	Weak transcription	HSMMtube	muscle
3	chr3:139673400-139695400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:139675000-139696600	Weak transcription	Ovary	ovary

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