Variant report

Variant	rs9284617
Chromosome Location	chr4:78992568-78992569
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78982293..78984651-chr4:78992521..78995488,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10000964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10005124	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10016866	1.00[ASN][1000 genomes]
rs1502887	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17002912	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17002918	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17002919	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17002923	0.91[EUR][1000 genomes]
rs2036460	0.86[MEX][hapmap]
rs28366819	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28367528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28446054	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28477353	0.91[EUR][1000 genomes]
rs28497565	0.91[EUR][1000 genomes]
rs28520643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28546473	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28566614	0.91[EUR][1000 genomes]
rs28723619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4340818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859517	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859895	1.00[CHB][hapmap]
rs6533375	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6842322	1.00[ASN][1000 genomes]
rs72858745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72858775	0.91[EUR][1000 genomes]
rs9284616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307331	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv967999	chr4:78991248-78995210	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9284617	G3BP2	cis	cerebellum	SCAN
rs9284617	SHROOM3	cis	cerebellum	SCAN
rs9284617	SCARB2	cis	parietal	SCAN
rs9284617	CXCL13	cis	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78980800-78998200	Weak transcription	Pancreas	Pancrea
2	chr4:78981000-78995600	Weak transcription	Fetal Intestine Small	intestine
3	chr4:78981200-79016600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:78982200-78998200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:78983400-78996000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:78983400-79001000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:78986200-78995600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr4:78987000-78995600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:78987200-78993200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:78987400-78994400	Weak transcription	Fetal Kidney	kidney
11	chr4:78988000-78992800	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:78988000-78994000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr4:78988600-78992800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr4:78988800-78992800	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr4:78988800-79002600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:78988800-79003000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr4:78989400-78992800	Strong transcription	HepG2	liver
18	chr4:78990200-78992800	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr4:78990800-78996000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr4:78991400-78995600	Weak transcription	Fetal Intestine Large	intestine
21	chr4:78991400-78996000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:78991400-79000600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:78991400-79000800	Weak transcription	Psoas Muscle	Psoas
24	chr4:78992000-78992800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:78992200-78993800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:78992200-78993800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:78992200-79006800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:78992400-78992800	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr4:78992400-78994400	Genic enhancers	HUES48 Cell Line	embryonic stem cell

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