Variant report

Variant	rs1547288
Chromosome Location	chr9:9310461-9310462
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10816081	0.95[CHB][hapmap];0.84[CHD][hapmap]
rs10816093	0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs1157904	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs12551223	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs1333106	0.92[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1981049	0.92[ASW][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.94[LWK][hapmap];0.81[MEX][hapmap]
rs2802280	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs4097905	0.91[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap]
rs4272446	0.95[CHB][hapmap]
rs4313205	0.82[JPT][hapmap]
rs4329321	0.91[CHB][hapmap]
rs4363255	0.81[JPT][hapmap]
rs4457389	0.80[CHB][hapmap]
rs4560852	0.82[CHB][hapmap]
rs4563945	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs4742581	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs4742583	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7042931	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7859634	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs7860238	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7863177	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9299091	0.84[JPT][hapmap]
rs9299092	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs9407413	0.97[ASN][1000 genomes]
rs9408753	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs953632	0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]

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	nsv498066	chr9:8961722-9486652	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv892249	chr9:9026854-9377679	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv892252	chr9:9164473-9476425	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1021440	chr9:9231961-9329870	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	n/a
5	nsv892254	chr9:9253587-9348102	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	n/a
6	nsv824847	chr9:9255377-9378016	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv613305	chr9:9263980-9310461	Enhancers Weak transcription	n/a	n/a	inside rSNPs	n/a
8	nsv892255	chr9:9264932-9348102	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	n/a
9	nsv892256	chr9:9269284-9348102	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	n/a
10	nsv1025791	chr9:9294304-9626331	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv892257	chr9:9304839-9349679	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	n/a
12	nsv892258	chr9:9304839-9455711	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1547288	PDCD1LG2	cis	parietal	SCAN
rs1547288	RLN2	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:9309800-9311200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:9310200-9310800	Enhancers	Pancreas	Pancrea
3	chr9:9310400-9310600	Enhancers	Stomach Mucosa	stomach

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