Variant report

Variant	rs4859517
Chromosome Location	chr4:78987403-78987404
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10000964	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10005124	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10016866	1.00[ASN][1000 genomes]
rs1502887	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17002912	0.93[EUR][1000 genomes]
rs17002918	0.93[EUR][1000 genomes]
rs17002919	0.93[EUR][1000 genomes]
rs17002923	0.90[EUR][1000 genomes]
rs28366819	0.93[EUR][1000 genomes]
rs28367528	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28446054	0.93[EUR][1000 genomes]
rs28477353	0.90[EUR][1000 genomes]
rs28497565	0.90[EUR][1000 genomes]
rs28520643	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28546473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28566614	0.90[EUR][1000 genomes]
rs28723619	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4340818	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	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72858775	0.90[EUR][1000 genomes]
rs9284616	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9284617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307331	0.95[AMR][1000 genomes];0.99[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	nsv1010714	chr4:78742505-78991030	Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4859517	SCARB2	cis	parietal	SCAN
rs4859517	G3BP2	cis	cerebellum	SCAN
rs4859517	SHROOM3	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78980800-78990000	Weak transcription	NHDF-Ad	bronchial
2	chr4:78980800-78990600	Weak transcription	Psoas Muscle	Psoas
3	chr4:78980800-78998200	Weak transcription	Pancreas	Pancrea
4	chr4:78981000-78990600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:78981000-78991200	Weak transcription	Right Atrium	heart
6	chr4:78981000-78995600	Weak transcription	Fetal Intestine Small	intestine
7	chr4:78981200-79016600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:78981400-78990400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr4:78982200-78990600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:78982200-78998200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:78983400-78996000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:78983400-79001000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:78984000-78990600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:78984200-78991000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:78984600-78990600	Weak transcription	HMEC	breast
16	chr4:78986200-78995600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:78986400-78988000	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr4:78986600-78988000	Enhancers	H1 Cell Line	embryonic stem cell
19	chr4:78987000-78995600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr4:78987200-78988000	Strong transcription	HepG2	liver
21	chr4:78987200-78990400	Weak transcription	Fetal Intestine Large	intestine
22	chr4:78987200-78993200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:78987400-78987600	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr4:78987400-78987800	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr4:78987400-78988000	Genic enhancers	HUES64 Cell Line	embryonic stem cell
26	chr4:78987400-78988000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr4:78987400-78988600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr4:78987400-78988600	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr4:78987400-78989600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:78987400-78994400	Weak transcription	Fetal Kidney	kidney

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