Variant report

Variant	rs13065319
Chromosome Location	chr3:20032624-20032625
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:19987801..19990677-chr3:20032427..20034907,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163576	Chromatin interaction
ENSG00000144566	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11128927	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11128928	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11128929	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11128930	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11128931	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1143451	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12629485	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12631435	0.87[EUR][1000 genomes]
rs13068289	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13072891	0.90[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs13076973	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13077307	0.81[ASN][1000 genomes]
rs13078505	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13082980	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13086159	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13089853	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13093485	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13097697	0.92[EUR][1000 genomes]
rs13098388	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17181400	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17181862	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17796115	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34305656	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34343204	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34417128	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34705953	0.84[ASN][1000 genomes]
rs34872212	0.86[EUR][1000 genomes]
rs35175665	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35482904	0.91[ASN][1000 genomes]
rs35684714	0.86[EUR][1000 genomes]
rs35713165	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4610240	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs59086970	0.83[ASN][1000 genomes]
rs59608170	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60255931	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796425	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71316239	0.92[EUR][1000 genomes]
rs7434271	0.92[EUR][1000 genomes]
rs7614695	0.88[ASN][1000 genomes]
rs7615145	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7618928	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7633940	0.88[ASN][1000 genomes]
rs7634934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7643167	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7646128	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9877801	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878879	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription 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	17 gene(s)	inside rSNPs	diseases
2	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats 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	17 gene(s)	inside rSNPs	diseases
6	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	nsv997486	chr3:20006702-20113989	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13065319	EFHB	cis	Artery Tibial	GTEx
rs13065319	EFHB	cis	Skin Sun Exposed Lower leg	GTEx
rs13065319	EFHB	cis	cerebellum	SCAN
rs13065319	EFHB	cis	parietal	SCAN
rs13065319	EFHB	cis	Muscle Skeletal	GTEx
rs13065319	EFHB	cis	normal skin	skin_eQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20008800-20035600	Weak transcription	Psoas Muscle	Psoas
2	chr3:20012400-20033600	Weak transcription	Fetal Brain Male	brain
3	chr3:20023000-20045800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:20024000-20041400	Weak transcription	Ovary	ovary
5	chr3:20024200-20033200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:20024200-20033400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:20024200-20036800	Weak transcription	Aorta	Aorta
8	chr3:20024200-20051400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:20024400-20034000	Weak transcription	Brain Germinal Matrix	brain
10	chr3:20025400-20033200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:20025600-20033400	Weak transcription	Brain Angular Gyrus	brain
12	chr3:20026400-20040800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:20027200-20033000	Weak transcription	Fetal Intestine Large	intestine
14	chr3:20027400-20036200	Weak transcription	NH-A	brain
15	chr3:20027600-20033400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:20027600-20033400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:20027600-20036000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:20030000-20035000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:20030000-20038600	Weak transcription	Fetal Thymus	thymus

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