Variant report

Variant	rs213387
Chromosome Location	chr3:60308293-60308294
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10510839	0.93[JPT][hapmap]
rs10866035	0.82[EUR][1000 genomes]
rs11130766	0.93[JPT][hapmap]
rs12494639	0.93[JPT][hapmap]
rs12498046	0.93[JPT][hapmap]
rs1546830	0.92[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs1569348	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1569349	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1569352	0.96[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs1882898	0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1882899	0.88[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1882900	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1882901	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs213383	0.88[ASN][1000 genomes]
rs213384	1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs213385	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34717494	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4679476	0.81[CEU][hapmap]
rs6446120	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6762886	0.81[CHD][hapmap]
rs6764498	0.81[CEU][hapmap]
rs6773826	0.92[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs6799964	0.80[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap]
rs727476	0.93[JPT][hapmap]
rs926143	0.81[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs963685	0.92[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs9815526	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9837070	0.86[JPT][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv590387	chr3:59890976-60481459	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1009971	chr3:60070974-60397331	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv529602	chr3:60088353-60830769	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010969	chr3:60124962-60425297	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv2422232	chr3:60192201-60334555	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv876844	chr3:60256485-60362565	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv876845	chr3:60256485-60367607	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1001134	chr3:60262617-60344190	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv590394	chr3:60289140-60388900	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv999794	chr3:60301059-60332871	Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv1011408	chr3:60307954-60417143	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs213387	IL17RD	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60296000-60312200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:60302600-60309200	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:60302600-60309200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:60302600-60311400	Weak transcription	Fetal Lung	lung
5	chr3:60307400-60309200	Enhancers	Liver	Liver
6	chr3:60308200-60311400	Weak transcription	Fetal Intestine Large	intestine

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