Variant report

Variant	rs4657570
Chromosome Location	chr1:166554578-166554579
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:166541145..166543068-chr1:166552578..166555523,2	K562	blood:
2	chr1:166553441..166555941-chr1:166692722..166694602,2	K562	blood:
3	chr1:166538818..166541010-chr1:166552416..166555173,2	K562	blood:
4	chr1:166552621..166555359-chr1:166806304..166809167,2	K562	blood:
5	chr1:166546817..166549594-chr1:166554279..166555815,3	K562	blood:

Variant related genes	Relation type
ENSG00000143157	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10918536	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10918549	0.91[ASW][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap]
rs1631056	0.82[CHD][hapmap];0.83[GIH][hapmap];0.85[ASN][1000 genomes]
rs17472904	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2119900	0.84[AMR][1000 genomes]
rs3125820	0.85[ASN][1000 genomes]
rs4514220	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs4657571	0.84[AMR][1000 genomes]
rs4657581	0.85[TSI][hapmap]
rs471764	0.85[CHB][hapmap];0.91[ASN][1000 genomes]
rs472652	0.91[ASN][1000 genomes]
rs473746	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs475264	0.85[ASN][1000 genomes]
rs476048	0.85[ASN][1000 genomes]
rs482782	0.84[ASN][1000 genomes]
rs482850	0.84[ASN][1000 genomes]
rs482905	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs483138	0.87[ASN][1000 genomes]
rs484070	0.82[CHB][hapmap];0.87[ASN][1000 genomes]
rs496095	0.82[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap]
rs497142	0.85[ASN][1000 genomes]
rs500437	0.85[ASN][1000 genomes]
rs500568	0.82[CHB][hapmap];0.87[ASN][1000 genomes]
rs503960	0.84[ASN][1000 genomes]
rs505012	0.82[CHB][hapmap];0.89[ASN][1000 genomes]
rs505135	0.82[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.87[ASN][1000 genomes]
rs511809	0.87[ASN][1000 genomes]
rs514307	0.87[ASN][1000 genomes]
rs519135	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs524397	0.85[ASN][1000 genomes]
rs525948	0.91[ASN][1000 genomes]
rs527241	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs529740	0.82[CHB][hapmap];0.86[GIH][hapmap];0.87[ASN][1000 genomes]
rs530513	0.82[CHD][hapmap];0.83[GIH][hapmap]
rs530690	0.82[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.87[ASN][1000 genomes]
rs532412	0.87[ASN][1000 genomes]
rs535889	0.85[ASN][1000 genomes]
rs536773	0.85[ASN][1000 genomes]
rs537720	0.89[ASN][1000 genomes]
rs537782	0.87[ASN][1000 genomes]
rs553928	0.82[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.85[ASN][1000 genomes]
rs556269	0.91[ASN][1000 genomes]
rs563206	0.83[JPT][hapmap]
rs568776	0.87[ASN][1000 genomes]
rs568821	0.87[ASN][1000 genomes]
rs571669	0.82[CHB][hapmap];0.83[GIH][hapmap]
rs579545	0.82[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.87[ASN][1000 genomes]
rs580432	0.82[CHB][hapmap];0.87[ASN][1000 genomes]
rs6427018	1.00[ASN][1000 genomes]
rs7539202	0.80[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	esv2757759	chr1:166491879-166650985	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv2758975	chr1:166491879-166650985	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv872511	chr1:166505186-166590046	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv872512	chr1:166532565-166581706	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv872513	chr1:166532565-166590046	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv872514	chr1:166532565-166595209	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv872515	chr1:166532565-166595692	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv872516	chr1:166536198-166590046	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv872517	chr1:166539001-166590046	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	esv2756869	chr1:166543542-166601778	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv872519	chr1:166545275-166616786	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv872518	chr1:166545275-166623180	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	esv34401	chr1:166546342-166617601	Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv872520	chr1:166546851-166590046	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4657570	MGST3	cis	cerebellum	SCAN
rs4657570	RGS4	cis	parietal	SCAN
rs4657570	MAEL	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166552400-166554600	Enhancers	K562	blood
2	chr1:166553800-166554800	Enhancers	Fetal Heart	heart
3	chr1:166554200-166554800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:166554400-166555000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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