Variant report

Variant	rs12738964
Chromosome Location	chr1:93274450-93274451
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11164803	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164814	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11164816	1.00[ASN][1000 genomes]
rs11164820	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164857	1.00[CHB][hapmap]
rs11577426	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11578004	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11578098	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11581705	1.00[ASN][1000 genomes]
rs11583778	1.00[ASN][1000 genomes]
rs11586570	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes]
rs11589122	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11800409	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11800771	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11800848	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs11803097	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11805007	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11810111	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11810217	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12081675	1.00[JPT][hapmap]
rs12728322	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap]
rs12731107	1.00[JPT][hapmap]
rs12743005	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12746893	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs12747275	1.00[JPT][hapmap]
rs12749786	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs1415296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs17381426	1.00[CHB][hapmap]
rs17614449	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1854797	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs2893226	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes]
rs34202284	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34244251	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap]
rs34250288	1.00[ASN][1000 genomes]
rs35031391	0.84[AMR][1000 genomes]
rs35183060	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs35901796	1.00[ASN][1000 genomes]
rs3790450	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4642892	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs59864761	1.00[ASN][1000 genomes]
rs6604026	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap]
rs66649041	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687931	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71652507	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514280	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap]
rs7521417	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv947289	chr1:93251307-93276080	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv530047	chr1:93273425-93308213	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12738964	FAM69A	cis	cerebellum	SCAN
rs12738964	FAM69A	cis	Artery Tibial	GTEx
rs12738964	FAM69A	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93271000-93276000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:93271800-93276800	Weak transcription	K562	blood
3	chr1:93272600-93276000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:93273000-93275000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:93273000-93275200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:93273400-93275000	Enhancers	HMEC	breast
7	chr1:93273400-93275000	Enhancers	NHEK	skin
8	chr1:93273600-93274600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr1:93273600-93275000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:93273600-93275000	Enhancers	Placenta	Placenta
11	chr1:93273600-93275000	Enhancers	Hela-S3	cervix
12	chr1:93274000-93275800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:93274200-93274600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:93274400-93274600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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