Variant report

Variant	rs9296592
Chromosome Location	chr6:13055406-13055407
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11961962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13190774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13193716	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13200673	0.94[EUR][1000 genomes]
rs13204304	0.94[EUR][1000 genomes]
rs13205551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13205960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13209107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13215349	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13218974	0.89[EUR][1000 genomes]
rs13219842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13220000	0.81[EUR][1000 genomes]
rs34054185	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34267578	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34381599	0.97[EUR][1000 genomes]
rs34952336	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35229766	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35273948	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35305875	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35776201	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36119782	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4132044	0.89[EUR][1000 genomes]
rs4361612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4373361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4379290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4580848	0.89[EUR][1000 genomes]
rs4615376	0.97[EUR][1000 genomes]
rs4711908	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4711909	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4711910	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4715064	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs4715072	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715082	0.94[EUR][1000 genomes]
rs6458616	1.00[CEU][hapmap];0.89[TSI][hapmap];0.96[EUR][1000 genomes]
rs6932757	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7738252	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7743585	0.89[CEU][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes]
rs7750023	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs7750099	0.89[CEU][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7750120	0.96[EUR][1000 genomes]
rs7756776	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7762827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775103	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9463377	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9463408	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9463423	0.97[EUR][1000 genomes]
rs9473285	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs9473354	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9473370	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9473427	0.93[EUR][1000 genomes]
rs9473436	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3521000	chr6:12561306-13128519	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3521001	chr6:12561306-13128519	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv817350	chr6:12922859-13137655	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv600992	chr6:12961922-13218549	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9296592	ERVFRDE1	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13029800-13056400	Weak transcription	Pancreas	Pancrea
2	chr6:13030000-13056400	Weak transcription	Brain Germinal Matrix	brain
3	chr6:13039400-13071600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr6:13040000-13058000	Weak transcription	Fetal Brain Male	brain
5	chr6:13048400-13063400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:13048600-13058000	Weak transcription	Lung	lung
7	chr6:13052200-13060600	Weak transcription	Aorta	Aorta
8	chr6:13052400-13066600	Weak transcription	Right Ventricle	heart
9	chr6:13052600-13063400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:13053400-13059400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:13053800-13058000	Weak transcription	Fetal Heart	heart
12	chr6:13054000-13061200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:13054200-13056200	Strong transcription	Primary hematopoietic stem cells	blood
14	chr6:13054400-13060200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:13054400-13071800	Weak transcription	Brain Hippocampus Middle	brain
16	chr6:13054600-13058000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:13054800-13074600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr6:13055200-13055600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:13055200-13056400	Weak transcription	Left Ventricle	heart
20	chr6:13055200-13060600	Weak transcription	Brain Anterior Caudate	brain
21	chr6:13055200-13073000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:13055200-13076400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr6:13055400-13059400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:13055400-13059400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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