Variant report

Variant	rs1533208
Chromosome Location	chr3:110155172-110155173
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1022229	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10934040	0.89[EUR][1000 genomes]
rs11715486	0.81[ASN][1000 genomes]
rs12487462	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs12633463	0.82[ASN][1000 genomes]
rs12637928	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13058952	0.82[ASN][1000 genomes]
rs13080207	0.89[EUR][1000 genomes]
rs13081130	0.82[ASN][1000 genomes]
rs13093393	0.81[ASN][1000 genomes]
rs1398346	0.80[CHB][hapmap];0.81[CHD][hapmap]
rs1398354	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs1398410	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1512681	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17727387	0.82[ASN][1000 genomes]
rs2055966	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs2063567	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2203187	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2399335	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs34998073	0.82[ASN][1000 genomes]
rs35156093	0.80[ASN][1000 genomes]
rs4682589	0.80[ASN][1000 genomes]
rs4682590	0.81[ASN][1000 genomes]
rs6771696	0.81[ASN][1000 genomes]
rs6788158	0.82[ASN][1000 genomes]
rs73209549	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7627779	0.86[EUR][1000 genomes]
rs7640755	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs963346	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9813893	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs9815868	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs9818091	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9843950	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs9851821	0.88[ASN][1000 genomes]
rs9862336	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9870835	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877332	chr3:109575764-110186611	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv460818	chr3:110007205-110155824	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv591272	chr3:110007205-110155824	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv829669	chr3:110022724-110188397	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv460819	chr3:110080893-110194026	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv470838	chr3:110083045-110194026	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv591273	chr3:110087264-110194026	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv877337	chr3:110091627-110186611	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv999414	chr3:110103126-110340180	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv1838188	chr3:110134108-110173739	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv829670	chr3:110134650-110308256	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv520365	chr3:110155172-110441165	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1533208	GUCA1C	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110153800-110157200	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr3:110154600-110157400	Enhancers	HepG2	liver
3	chr3:110154800-110156000	Enhancers	Fetal Intestine Large	intestine
4	chr3:110155000-110155600	Flanking Active TSS	Liver	Liver

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