Variant report

Variant	rs3766208
Chromosome Location	chr1:47268526-47268527
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47264251..47266259-chr1:47267707..47269923,2	K562	blood:
2	chr1:47221048..47223209-chr1:47267479..47269912,2	MCF-7	breast:
3	chr1:47263919..47266818-chr1:47267658..47269946,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142973	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10493125	0.95[EUR][1000 genomes]
rs11211362	0.84[ASN][1000 genomes]
rs11211370	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11211375	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11211376	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11211377	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12135031	0.86[ASN][1000 genomes]
rs12142787	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.99[ASN][1000 genomes]
rs12733133	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12742610	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2297809	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2297810	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2297811	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2297813	0.84[ASW][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs35191195	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35333582	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35947953	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3766194	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3766209	1.00[MEX][hapmap]
rs4646480	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4646481	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4646484	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4646491	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56101164	0.90[EUR][1000 genomes]
rs6658037	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66871510	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6700251	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72681937	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7535312	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers 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	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1011086	chr1:47259078-47305191	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv870792	chr1:47259138-47272185	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv870538	chr1:47259138-47309265	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1010063	chr1:47264205-47285118	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv546165	chr1:47266590-47272785	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3766208	FOXE3	cis	parietal	SCAN
rs3766208	PRDX1	cis	parietal	SCAN
rs3766208	BEND5	cis	cerebellum	SCAN
rs3766208	CYP4B1	cis	lung	GTEx
rs3766208	UROD	cis	cerebellum	SCAN
rs3766208	CYP4B1	cis	Esophagus Muscularis	GTEx
rs3766208	CYP4B1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47264600-47269200	Active TSS	Left Ventricle	heart
2	chr1:47265400-47268600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr1:47265400-47271400	Weak transcription	Fetal Intestine Small	intestine
4	chr1:47265600-47268800	Active TSS	Psoas Muscle	Psoas
5	chr1:47265600-47271800	Weak transcription	Spleen	Spleen
6	chr1:47265600-47279200	Weak transcription	Gastric	stomach
7	chr1:47265800-47269800	Weak transcription	Right Atrium	heart
8	chr1:47266400-47269200	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr1:47266400-47273800	Enhancers	Placenta	Placenta
10	chr1:47266800-47271600	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:47267200-47268600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr1:47267800-47273000	Enhancers	Esophagus	oesophagus
13	chr1:47267800-47273600	Enhancers	Lung	lung
14	chr1:47268000-47271600	Weak transcription	Fetal Intestine Large	intestine
15	chr1:47268200-47269600	Weak transcription	Stomach Mucosa	stomach
16	chr1:47268400-47270000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
17	chr1:47268400-47273600	Enhancers	Placenta Amnion	Placenta Amnion

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