Variant report

Variant	rs9390251
Chromosome Location	chr6:145216876-145216877
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:145199307..145201397-chr6:145215115..145217715,2	MCF-7	breast:
2	chr6:145201337..145203638-chr6:145216536..145219357,2	MCF-7	breast:
3	chr6:145215634..145217242-chr6:145456840..145459220,2	MCF-7	breast:
4	chr6:145210923..145212956-chr6:145216545..145218194,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11969748	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12174209	0.86[EUR][1000 genomes]
rs13195749	0.90[ASN][1000 genomes]
rs13210332	0.95[EUR][1000 genomes]
rs1338704	0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs1338705	0.86[ASN][1000 genomes]
rs2050719	0.86[ASN][1000 genomes]
rs35285375	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35946718	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4323328	0.96[EUR][1000 genomes]
rs4487599	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4896762	0.87[ASN][1000 genomes]
rs57337295	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6570656	0.90[EUR][1000 genomes]
rs6913165	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71547172	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7769009	0.81[CHB][hapmap]
rs7769065	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9285505	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9322003	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9322004	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9322005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9373433	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9373434	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9376869	0.91[EUR][1000 genomes]
rs9376874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9386089	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9390243	0.89[EUR][1000 genomes]
rs9390252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9390253	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9390254	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9390257	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9399514	0.91[EUR][1000 genomes]
rs9399517	0.83[ASN][1000 genomes]
rs9399519	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9399520	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9403621	0.94[EUR][1000 genomes]
rs9403627	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9403628	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9403629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9403631	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9403633	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9403634	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9497120	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9497121	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9497132	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv1850377	chr6:145199259-145319640	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9390251	PLAGL1	cis	cerebellum	SCAN
rs9390251	VTA1	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145210600-145217000	Weak transcription	Right Atrium	heart
2	chr6:145214800-145218400	Weak transcription	Fetal Intestine Large	intestine
3	chr6:145215400-145218000	Weak transcription	HSMMtube	muscle
4	chr6:145215400-145220800	Enhancers	Osteobl	bone
5	chr6:145215800-145217600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:145215800-145218400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:145216000-145217200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:145216000-145217200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:145216400-145217600	Weak transcription	A549	lung
10	chr6:145216400-145221200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:145216600-145219200	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr6:145216800-145217800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr6:145216800-145218600	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr6:145216800-145218800	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr6:145216800-145219000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr6:145216800-145219200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:145216800-145222400	Enhancers	NHDF-Ad	bronchial

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