Variant report

Variant	rs9473427
Chromosome Location	chr6:13078644-13078645
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13076579..13079092-chr6:13614860..13616733,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225921	Chromatin interaction
ENSG00000261071	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11961962	1.00[CEU][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs13190774	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs13192747	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs13193716	0.91[EUR][1000 genomes]
rs13200673	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13204304	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13205551	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13205960	1.00[CEU][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs13209107	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs13215349	0.87[EUR][1000 genomes]
rs13218974	0.84[EUR][1000 genomes]
rs13219842	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17375327	0.92[JPT][hapmap]
rs1937766	1.00[JPT][hapmap]
rs1937768	0.92[JPT][hapmap]
rs34054185	0.91[EUR][1000 genomes]
rs34267578	0.87[EUR][1000 genomes]
rs34381599	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34952336	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35229766	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35273948	0.91[EUR][1000 genomes]
rs35305875	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35776201	0.87[EUR][1000 genomes]
rs36119782	0.93[EUR][1000 genomes]
rs4132044	0.84[EUR][1000 genomes]
rs4361612	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4373361	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4379290	1.00[CEU][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs4580848	0.85[EUR][1000 genomes]
rs4615376	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711908	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4711909	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4711910	1.00[CEU][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4715064	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4715072	0.91[EUR][1000 genomes]
rs4715082	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6458616	1.00[CEU][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.87[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6458639	0.92[JPT][hapmap]
rs6458641	0.83[JPT][hapmap]
rs6921616	1.00[JPT][hapmap]
rs6932757	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7738252	1.00[CEU][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7740162	0.92[JPT][hapmap]
rs7743585	0.89[CEU][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs7744129	0.92[JPT][hapmap]
rs7750023	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs7750099	0.89[CEU][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs7750120	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7756776	0.88[EUR][1000 genomes]
rs7762827	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7769033	0.92[JPT][hapmap]
rs7775103	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs9296592	1.00[CEU][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs9463377	1.00[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs9463408	1.00[CEU][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9463423	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9473285	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9473354	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9473370	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9473429	0.89[ASW][hapmap];0.94[LWK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs9473435	0.89[ASW][hapmap];0.83[YRI][hapmap]
rs9473436	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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
rs9473427	ERVFRDE1	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13069800-13082200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr6:13072600-13082200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:13075000-13079400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr6:13075200-13082600	Enhancers	Brain Anterior Caudate	brain
5	chr6:13075400-13079600	Enhancers	Left Ventricle	heart
6	chr6:13075600-13079200	Enhancers	Right Ventricle	heart
7	chr6:13076600-13078800	Enhancers	Right Atrium	heart
8	chr6:13076800-13078800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:13076800-13080400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr6:13076800-13082000	Weak transcription	Brain Angular Gyrus	brain
11	chr6:13077000-13079400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:13077000-13079400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:13077000-13080600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:13077000-13081600	Enhancers	Fetal Heart	heart
15	chr6:13077600-13081400	Weak transcription	Brain Hippocampus Middle	brain
16	chr6:13077800-13079200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:13077800-13081000	Enhancers	Aorta	Aorta
18	chr6:13078400-13079000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:13078400-13079000	Enhancers	HSMMtube	muscle
20	chr6:13078400-13079200	Enhancers	H1 Cell Line	embryonic stem cell
21	chr6:13078400-13079400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:13078400-13079600	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr6:13078400-13079600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:13078400-13080000	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr6:13078600-13079200	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr6:13078600-13079200	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr6:13078600-13079400	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr6:13078600-13079600	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr6:13078600-13080800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:13078600-13101400	Weak transcription	Lung	lung

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