Variant report

Variant	rs17420118
Chromosome Location	chr4:79075964-79075965
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10000651	0.94[ASN][1000 genomes]
rs10002604	0.81[ASN][1000 genomes]
rs10003965	0.84[ASN][1000 genomes]
rs10004159	0.84[ASN][1000 genomes]
rs10005735	0.84[ASN][1000 genomes]
rs10007371	0.90[ASN][1000 genomes]
rs10023697	0.88[ASN][1000 genomes]
rs10025194	0.84[ASN][1000 genomes]
rs10025611	0.84[ASN][1000 genomes]
rs10025977	0.84[ASN][1000 genomes]
rs10026268	0.84[ASN][1000 genomes]
rs10028988	0.84[ASN][1000 genomes]
rs10518194	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[ASN][1000 genomes]
rs13133346	0.84[ASN][1000 genomes]
rs13136410	0.84[ASN][1000 genomes]
rs13150598	0.88[ASN][1000 genomes]
rs1317018	0.84[ASN][1000 genomes]
rs16997130	0.84[ASN][1000 genomes]
rs17418552	0.90[ASN][1000 genomes]
rs17419053	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17420328	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1878437	0.84[ASN][1000 genomes]
rs2078481	0.84[ASN][1000 genomes]
rs28409486	0.87[ASN][1000 genomes]
rs28542863	0.97[ASN][1000 genomes]
rs28597965	0.84[ASN][1000 genomes]
rs2867004	0.90[ASN][1000 genomes]
rs28671092	0.84[ASN][1000 genomes]
rs28750077	0.90[ASN][1000 genomes]
rs2903452	0.84[ASN][1000 genomes]
rs34552897	0.84[ASN][1000 genomes]
rs35374567	0.84[ASN][1000 genomes]
rs35967777	1.00[ASN][1000 genomes]
rs55690666	0.84[ASN][1000 genomes]
rs56368720	0.84[ASN][1000 genomes]
rs58118093	0.90[ASN][1000 genomes]
rs58970756	0.90[ASN][1000 genomes]
rs66631138	0.84[ASN][1000 genomes]
rs67819118	0.82[EUR][1000 genomes]
rs6838661	0.94[ASN][1000 genomes]
rs6840357	0.84[ASN][1000 genomes]
rs6848061	1.00[ASN][1000 genomes]
rs6858810	0.84[ASN][1000 genomes]
rs72654668	0.97[ASN][1000 genomes]
rs7670625	0.84[ASN][1000 genomes]
rs7673873	0.84[ASN][1000 genomes]
rs7677432	0.84[ASN][1000 genomes]
rs7681238	0.84[ASN][1000 genomes]
rs7695979	0.84[ASN][1000 genomes]
rs7698326	0.88[ASN][1000 genomes]
rs7699120	0.84[ASN][1000 genomes]
rs9307352	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv525530	chr4:79024524-79266563	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv879502	chr4:79052851-79144309	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1010782	chr4:79057839-79387207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17420118	SCARB2	cis	parietal	SCAN
rs17420118	SDAD1	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79067200-79078000	Weak transcription	Psoas Muscle	Psoas
2	chr4:79071000-79083600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:79071200-79078000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:79071200-79082600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr4:79071400-79077200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:79071400-79078000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:79071400-79096600	Weak transcription	Pancreas	Pancrea
8	chr4:79071600-79076600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:79072000-79076800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:79072600-79076000	Enhancers	HepG2	liver
11	chr4:79072800-79076000	Weak transcription	Fetal Lung	lung
12	chr4:79073200-79076800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:79073400-79076000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr4:79073400-79076800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr4:79073600-79082000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:79073800-79077200	Enhancers	Fetal Heart	heart
17	chr4:79074000-79076800	Weak transcription	Fetal Kidney	kidney
18	chr4:79074400-79076000	Weak transcription	Fetal Intestine Large	intestine
19	chr4:79074400-79076200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr4:79074400-79076200	Weak transcription	Fetal Intestine Small	intestine
21	chr4:79074400-79077800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:79075400-79078400	Enhancers	H1 Cell Line	embryonic stem cell
23	chr4:79075600-79078200	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr4:79075800-79078200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:79075800-79078400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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