Variant report

Variant	rs6594713
Chromosome Location	chr5:112715374-112715375
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112714439..112715552-chr5:112846186..112846977,5	MCF-7	breast:

Extended variants
information (count: 128 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10035558	0.87[YRI][hapmap]
rs10035647	0.82[YRI][hapmap]
rs10038521	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10051115	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10053341	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10061462	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10065790	0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs10076511	0.87[YRI][hapmap]
rs10434754	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.86[ASN][1000 genomes]
rs10477490	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241199	0.87[YRI][hapmap]
rs1157696	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs13154300	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13159509	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13164135	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13164326	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13170435	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13171482	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13171630	0.81[ASN][1000 genomes]
rs13174075	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13174151	0.90[ASN][1000 genomes]
rs13174206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13177853	0.86[ASN][1000 genomes]
rs13180516	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13180522	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13181534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13181732	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13181944	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13182972	1.00[CHB][hapmap]
rs13183383	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13184538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13187823	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13189050	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13189910	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13436825	0.81[ASN][1000 genomes]
rs1602862	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17325307	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[ASN][1000 genomes]
rs17325503	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17325825	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17327964	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17331844	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs17388260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17389165	1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs1816062	0.81[ASN][1000 genomes]
rs1838206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1922678	1.00[JPT][hapmap]
rs1922679	0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs2248930	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs34316732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34558181	0.86[ASN][1000 genomes]
rs34682492	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs348928	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs348929	0.86[CHB][hapmap]
rs348930	0.86[CHB][hapmap]
rs348931	0.86[CHB][hapmap]
rs348932	0.86[CHB][hapmap]
rs348947	0.86[CHB][hapmap]
rs348956	0.86[CHB][hapmap]
rs348961	0.86[CHB][hapmap]
rs348962	0.86[CHB][hapmap]
rs348963	0.86[CHB][hapmap]
rs34951736	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35359071	0.95[ASN][1000 genomes]
rs35886114	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35926701	0.81[ASN][1000 genomes]
rs35933960	0.81[ASN][1000 genomes]
rs36023163	0.81[ASN][1000 genomes]
rs367943	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs4438866	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs444322	0.86[CHB][hapmap]
rs455435	0.86[CHB][hapmap]
rs460079	0.86[CHB][hapmap]
rs463167	0.86[CHB][hapmap]
rs463249	0.86[CHB][hapmap]
rs56180725	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58268366	0.86[ASN][1000 genomes]
rs644154	0.86[CHB][hapmap]
rs6594706	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6594714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6594715	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6594716	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66572866	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67320720	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67693032	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6861940	0.82[YRI][hapmap]
rs6867579	1.00[CHB][hapmap];0.88[GIH][hapmap];0.81[ASN][1000 genomes]
rs6870401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6871934	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6872490	0.90[ASN][1000 genomes]
rs6874175	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6876848	0.82[CEU][hapmap]
rs6879776	0.87[YRI][hapmap]
rs6880562	0.95[ASN][1000 genomes]
rs6883102	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6887482	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6887914	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6889489	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6890874	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6894687	0.82[CEU][hapmap]
rs6896843	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71577442	0.86[ASN][1000 genomes]
rs71577447	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71577448	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72792189	0.86[ASN][1000 genomes]
rs7701895	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[ASN][1000 genomes]
rs7702837	0.85[YRI][hapmap]
rs7706721	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7708947	0.87[YRI][hapmap]
rs7709646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7714221	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7714760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7717630	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7718203	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs7718616	1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7720414	0.81[ASN][1000 genomes]
rs7725712	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7727056	0.90[ASN][1000 genomes]
rs7727501	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs7729269	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][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]
rs7731231	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734576	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7737512	0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[ASN][1000 genomes]
rs8180416	1.00[CHB][hapmap]
rs9326890	0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap]
rs9326891	0.80[CEU][hapmap]
rs9716322	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv949165	chr5:112615626-112730216	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Brain cytoarchitecture	20308991	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6594713	REEP5	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112700800-112718000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:112707800-112719000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:112708000-112716200	Weak transcription	Fetal Kidney	kidney
4	chr5:112711400-112716200	Weak transcription	NH-A	brain
5	chr5:112711800-112716200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:112712600-112715400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr5:112712600-112715800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr5:112713000-112715400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr5:112714000-112717000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:112714200-112715600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr5:112714200-112717000	Enhancers	Fetal Stomach	stomach
12	chr5:112714400-112715600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr5:112714400-112716200	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr5:112714400-112717200	Enhancers	Fetal Heart	heart
15	chr5:112714600-112716400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr5:112714600-112717000	Enhancers	Fetal Lung	lung
17	chr5:112714800-112715600	Enhancers	Primary T cells from cord blood	blood
18	chr5:112714800-112718600	Enhancers	Dnd41	blood
19	chr5:112715000-112715400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr5:112715000-112716200	Enhancers	Rectal Smooth Muscle	rectum
21	chr5:112715000-112716400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:112715000-112720600	Weak transcription	Aorta	Aorta
23	chr5:112715200-112715600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr5:112715200-112716000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:112715200-112716200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr5:112715200-112716200	Weak transcription	HMEC	breast
27	chr5:112715200-112716800	Weak transcription	NHEK	skin
28	chr5:112715200-112718200	Weak transcription	HUVEC	blood vessel

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