Variant report

Variant	rs1317018
Chromosome Location	chr4:79056713-79056714
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10000651	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10002604	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10003965	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10004159	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10005735	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10005862	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10007371	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10018454	0.94[ASN][1000 genomes]
rs10023697	0.85[ASN][1000 genomes]
rs10025194	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025611	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025769	0.90[ASN][1000 genomes]
rs10025977	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10026268	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10028988	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10030639	0.94[ASN][1000 genomes]
rs10033428	0.94[ASN][1000 genomes]
rs10213063	0.94[ASN][1000 genomes]
rs10213609	0.94[ASN][1000 genomes]
rs10518194	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13127746	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13133346	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13136410	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13144972	0.94[ASN][1000 genomes]
rs13150598	0.85[ASN][1000 genomes]
rs16997130	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17418552	0.93[ASN][1000 genomes]
rs17419053	0.93[ASN][1000 genomes]
rs17420118	0.84[ASN][1000 genomes]
rs17420328	0.84[ASN][1000 genomes]
rs1878437	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2078481	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28409486	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28479828	0.94[ASN][1000 genomes]
rs28542863	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs28597965	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28635454	0.94[ASN][1000 genomes]
rs2867004	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2867006	0.82[ASN][1000 genomes]
rs28671092	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28677913	0.94[ASN][1000 genomes]
rs28707182	0.94[ASN][1000 genomes]
rs28750077	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28822779	0.94[ASN][1000 genomes]
rs2903452	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34552897	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35060393	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35374567	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35967777	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4610363	0.94[ASN][1000 genomes]
rs4634250	0.94[ASN][1000 genomes]
rs55690666	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56368720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58118093	0.93[ASN][1000 genomes]
rs58969863	0.94[ASN][1000 genomes]
rs58970756	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66631138	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820400	0.94[ASN][1000 genomes]
rs6825089	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6838483	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6838661	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6840121	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6840357	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848061	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6857278	0.94[ASN][1000 genomes]
rs6857527	0.94[ASN][1000 genomes]
rs6858810	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71609399	0.85[ASN][1000 genomes]
rs72654668	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7666444	0.94[ASN][1000 genomes]
rs7670625	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7673873	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7677432	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7681238	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7684543	0.94[ASN][1000 genomes]
rs7695979	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698326	0.85[ASN][1000 genomes]
rs7699120	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307335	0.94[ASN][1000 genomes]
rs9307336	0.94[ASN][1000 genomes]
rs9307337	0.94[ASN][1000 genomes]
rs9307338	0.94[ASN][1000 genomes]
rs9307339	0.94[ASN][1000 genomes]
rs9307340	0.94[ASN][1000 genomes]
rs9307352	0.85[ASN][1000 genomes]
rs9991356	0.94[ASN][1000 genomes]
rs9994298	0.94[ASN][1000 genomes]
rs9994422	0.94[ASN][1000 genomes]
rs9999763	0.94[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	nsv520625	chr4:79002655-79071788	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1317018	SCARB2	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79047600-79057200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:79047600-79057400	Weak transcription	Pancreas	Pancrea
3	chr4:79050400-79056800	Enhancers	HepG2	liver
4	chr4:79051200-79060200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:79053000-79056800	Weak transcription	Psoas Muscle	Psoas
6	chr4:79053400-79058600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:79053800-79056800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr4:79053800-79057000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:79053800-79057000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr4:79053800-79058800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:79054000-79057200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:79054000-79068400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr4:79054000-79070400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:79056400-79057600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:79056400-79058200	Enhancers	Fetal Heart	heart
16	chr4:79056400-79061200	Enhancers	Fetal Intestine Large	intestine
17	chr4:79056600-79057200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr4:79056600-79058000	Enhancers	HSMMtube	muscle
19	chr4:79056600-79058200	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr4:79056600-79060800	Enhancers	Fetal Intestine Small	intestine

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