Variant report

Variant	rs17002918
Chromosome Location	chr4:78996302-78996303
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10000964	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10005124	0.93[EUR][1000 genomes]
rs1502887	0.90[EUR][1000 genomes]
rs17002912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17002919	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17002923	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28366819	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28367528	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28398889	0.83[JPT][hapmap]
rs28446054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28477353	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28497565	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28520643	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28546473	0.90[EUR][1000 genomes]
rs28566614	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28723619	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4340818	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4859517	0.93[EUR][1000 genomes]
rs72858745	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72858775	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9284616	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9284617	0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9307331	0.82[AMR][1000 genomes];0.94[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17002918	SCARB2	cis	parietal	SCAN
rs17002918	NSF	trans	lymphoblastoid	seeQTL
rs17002918	SHROOM3	cis	cerebellum	SCAN

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	chr4:78981200-79016600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:78982200-78998200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:78983400-79001000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:78988800-79002600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:78988800-79003000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr4:78991400-79000600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:78991400-79000800	Weak transcription	Psoas Muscle	Psoas
9	chr4:78992200-79006800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:78992800-78997600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr4:78994000-78999000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:78994800-78998400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:78995200-78996600	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr4:78995400-78997000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:78995400-78997200	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr4:78995400-78997800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr4:78995600-78996600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:78995600-78997000	Enhancers	Fetal Heart	heart
19	chr4:78995600-78997400	Enhancers	H1 Cell Line	embryonic stem cell
20	chr4:78995600-78997400	Enhancers	H9 Cell Line	embryonic stem cell
21	chr4:78995600-78998200	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr4:78995800-78997600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:78995800-79015800	Weak transcription	HepG2	liver
24	chr4:78996000-78996600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr4:78996000-78996800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr4:78996000-78997200	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr4:78996200-78996600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:78996200-78997400	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr4:78996200-79000400	Weak transcription	Fetal Kidney	kidney

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