Variant report

Variant	rs1882899
Chromosome Location	chr3:60310427-60310428
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:60302553..60304671-chr3:60309983..60311740,2	K562	blood:

Extended variants
information (count: 41 )
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	0.84[CHD][hapmap];0.93[JPT][hapmap]
rs1546830	0.96[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs1569348	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1569349	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1569352	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs1882898	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1882900	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882901	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs213383	0.87[ASN][1000 genomes]
rs213384	0.88[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs213385	0.83[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs213387	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]
rs34717494	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4679476	0.84[CEU][hapmap]
rs6446120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6762886	0.84[CHD][hapmap]
rs6764498	0.84[CEU][hapmap]
rs6773826	0.96[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs6799964	0.83[CHB][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap]
rs727476	0.81[CHD][hapmap];0.93[JPT][hapmap]
rs926143	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs963685	0.88[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs9815526	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9837070	0.86[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
13	nsv1011133	chr3:60309541-60417339	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1882899	IL17RD	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60296000-60312200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:60302600-60311400	Weak transcription	Fetal Lung	lung
3	chr3:60308200-60311400	Weak transcription	Fetal Intestine Large	intestine
4	chr3:60309000-60312200	Weak transcription	Lung	lung
5	chr3:60309200-60310800	Enhancers	Dnd41	blood
6	chr3:60309400-60312400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:60309400-60321600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:60309600-60311400	Weak transcription	K562	blood
9	chr3:60310000-60311200	Weak transcription	Fetal Stomach	stomach
10	chr3:60310400-60310600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:60310400-60310600	Enhancers	HUES64 Cell Line	embryonic stem cell

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