Variant report

Variant	rs9568413
Chromosome Location	chr13:51025399-51025400
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	chr13:50994481..50996784-chr13:51024058..51026768,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1028862	0.82[EUR][1000 genomes]
rs10492410	0.83[ASN][1000 genomes]
rs12428087	0.82[EUR][1000 genomes]
rs12428189	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12431131	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1327644	0.80[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1359860	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17074346	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17074358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1924372	0.86[EUR][1000 genomes]
rs1924373	0.81[EUR][1000 genomes]
rs201763	0.82[ASN][1000 genomes]
rs201777	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs201778	0.80[ASN][1000 genomes]
rs201781	0.82[ASN][1000 genomes]
rs201782	0.82[ASN][1000 genomes]
rs201783	0.82[ASN][1000 genomes]
rs201784	0.82[ASN][1000 genomes]
rs201786	0.82[ASN][1000 genomes]
rs201789	0.86[CHB][hapmap]
rs35824953	0.91[ASN][1000 genomes]
rs471315	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs56023535	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56075206	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58633776	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60379059	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61962133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61962135	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61964386	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67618912	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs719103	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7327154	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7334326	0.87[ASN][1000 genomes]
rs7983762	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7996632	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8000329	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8000875	0.86[EUR][1000 genomes]
rs8000921	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9316495	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9316496	0.83[ASN][1000 genomes]
rs9316497	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9562962	0.86[EUR][1000 genomes]
rs9562964	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9562965	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9562966	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9562967	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9562968	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9562970	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9562972	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9562973	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9562974	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9562975	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9562976	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9562980	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9562981	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9562982	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9568397	0.86[EUR][1000 genomes]
rs9568398	0.86[EUR][1000 genomes]
rs9568400	0.85[EUR][1000 genomes]
rs9568401	0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs9568402	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9568403	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9568404	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9568405	0.86[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs9568406	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568407	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568408	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568409	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568412	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568416	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9568417	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9568418	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9568419	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9568422	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9568423	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9568424	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9568425	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9568426	0.82[EUR][1000 genomes]
rs9568427	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9568428	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9568429	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9568430	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9568431	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9568433	0.86[CHB][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes]
rs9634832	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9634834	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv832609	chr13:50946577-51065968	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1045237	chr13:50976560-51102386	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51019600-51025800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr13:51021600-51025800	Weak transcription	Pancreas	Pancrea
3	chr13:51022000-51027200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr13:51022600-51034200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr13:51023000-51025400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr13:51023000-51026200	Weak transcription	Fetal Kidney	kidney
7	chr13:51023000-51027000	Weak transcription	Psoas Muscle	Psoas
8	chr13:51023200-51025600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr13:51023200-51025600	Weak transcription	Left Ventricle	heart
10	chr13:51023200-51026800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr13:51023200-51026800	Weak transcription	Fetal Heart	heart
12	chr13:51023200-51027000	Weak transcription	Fetal Muscle Leg	muscle
13	chr13:51023200-51027000	Weak transcription	Right Atrium	heart
14	chr13:51023200-51027200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr13:51023200-51027400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr13:51023200-51027400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr13:51023200-51030200	Weak transcription	Colon Smooth Muscle	Colon
18	chr13:51023400-51026200	Weak transcription	Brain Hippocampus Middle	brain
19	chr13:51023400-51026400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr13:51023400-51026800	Weak transcription	Adipose Nuclei	Adipose
21	chr13:51023400-51027000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr13:51023400-51027000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr13:51023600-51025600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr13:51023600-51025600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr13:51023600-51025600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr13:51023600-51025800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr13:51023600-51026800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr13:51023600-51027000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr13:51023600-51027000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr13:51023600-51027400	Weak transcription	HMEC	breast
31	chr13:51024600-51026400	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr13:51024600-51030200	Weak transcription	Aorta	Aorta
33	chr13:51024800-51026200	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr13:51025000-51026200	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr13:51025200-51025600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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