Variant report

Variant	rs2769813
Chromosome Location	chr9:97151194-97151195
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10821352	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs10993127	0.84[CHD][hapmap]
rs10993182	0.93[ASN][1000 genomes]
rs10993186	0.93[ASN][1000 genomes]
rs10993188	0.94[ASN][1000 genomes]
rs11525963	0.91[ASN][1000 genomes]
rs12235970	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs12236219	0.90[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap]
rs12236578	0.80[ASN][1000 genomes]
rs16909983	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16910109	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1752784	0.94[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1752786	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs2104642	0.90[ASN][1000 genomes]
rs2479615	0.81[CEU][hapmap]
rs2486632	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs2769805	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2769816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2809679	0.80[EUR][1000 genomes]
rs2809768	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2809774	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2993948	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3118790	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4398990	0.81[EUR][1000 genomes]
rs4518726	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4744338	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4744345	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs60964095	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs639276	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs7042481	0.86[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap]
rs7848227	0.81[JPT][hapmap]
rs7858082	0.86[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs9409544	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9409546	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs9409547	0.81[CEU][hapmap]
rs9409550	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9409764	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893592	chr9:96973995-97295269	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1046906	chr9:96999227-97239809	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv982324	chr9:97139062-97200156	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2769813	HIATL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97137800-97153000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr9:97138200-97162400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr9:97138400-97152800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr9:97138800-97152800	Weak transcription	Hela-S3	cervix
5	chr9:97138800-97168600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr9:97139000-97159600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:97147000-97159600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr9:97148200-97151400	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr9:97148600-97159600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr9:97148800-97165400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr9:97149000-97159600	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr9:97149200-97152400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr9:97149800-97153000	Weak transcription	Fetal Heart	heart
14	chr9:97150000-97159600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr9:97150000-97166200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:97150200-97160000	Weak transcription	K562	blood
17	chr9:97150600-97152400	Weak transcription	GM12878-XiMat	blood
18	chr9:97150800-97152800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr9:97150800-97159600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr9:97151000-97151600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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