Variant report

Variant	rs9568400
Chromosome Location	chr13:50958930-50958931
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	chr13:50947157..50949330-chr13:50957372..50959831,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs12428189	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12431131	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1327644	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1359860	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs149875	0.86[ASN][1000 genomes]
rs17074358	0.82[EUR][1000 genomes]
rs1924372	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1924373	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200222	0.88[ASN][1000 genomes]
rs200223	0.88[ASN][1000 genomes]
rs200224	0.88[ASN][1000 genomes]
rs201796	0.81[ASN][1000 genomes]
rs201798	0.81[ASN][1000 genomes]
rs3116625	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs35824953	0.84[ASN][1000 genomes]
rs430269	0.86[ASN][1000 genomes]
rs471315	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs56023535	0.87[EUR][1000 genomes]
rs56075206	0.87[EUR][1000 genomes]
rs58633776	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60379059	0.82[EUR][1000 genomes]
rs61962133	0.87[EUR][1000 genomes]
rs61962135	0.82[EUR][1000 genomes]
rs61964386	0.80[EUR][1000 genomes]
rs719103	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7327154	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7334326	0.80[ASN][1000 genomes]
rs7983762	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7996632	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8000329	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8000875	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8000921	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9316495	0.80[ASN][1000 genomes]
rs9562962	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9562963	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9562964	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9562965	0.84[ASN][1000 genomes]
rs9562966	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9562967	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9562968	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9562970	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9562972	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9562973	0.87[EUR][1000 genomes]
rs9562974	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9562980	0.80[EUR][1000 genomes]
rs9562981	0.80[EUR][1000 genomes]
rs9562982	0.80[EUR][1000 genomes]
rs9568397	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568398	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568399	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568402	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9568403	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9568404	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9568406	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9568407	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9568408	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9568409	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9568410	0.87[EUR][1000 genomes]
rs9568412	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9568413	0.85[EUR][1000 genomes]
rs9568414	0.85[EUR][1000 genomes]
rs9568415	0.85[EUR][1000 genomes]
rs9568422	0.80[EUR][1000 genomes]
rs9568423	0.80[EUR][1000 genomes]
rs9568424	0.80[EUR][1000 genomes]
rs9568425	0.80[EUR][1000 genomes]
rs9568427	0.80[EUR][1000 genomes]
rs9568428	0.80[EUR][1000 genomes]
rs9568429	0.80[EUR][1000 genomes]
rs9568430	0.80[EUR][1000 genomes]
rs9634832	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9634834	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50950400-50967200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:50951600-50961000	Weak transcription	Pancreas	Pancrea
3	chr13:50952800-50959600	Weak transcription	Fetal Heart	heart
4	chr13:50955600-50960400	Weak transcription	HepG2	liver
5	chr13:50956200-50960800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr13:50956600-50959000	Weak transcription	Left Ventricle	heart
7	chr13:50956600-50960000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr13:50956600-50961000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr13:50957000-50959600	Weak transcription	Fetal Muscle Leg	muscle
10	chr13:50957400-50960600	Weak transcription	Right Ventricle	heart
11	chr13:50958200-50960000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr13:50958600-50959000	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr13:50958600-50959200	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr13:50958600-50959800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr13:50958600-50959800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr13:50958600-50959800	Enhancers	Liver	Liver
17	chr13:50958600-50960000	Enhancers	Primary T cells from cord blood	blood
18	chr13:50958600-50961800	Enhancers	Thymus	Thymus
19	chr13:50958600-50961800	Enhancers	Dnd41	blood
20	chr13:50958600-50962800	Enhancers	Fetal Thymus	thymus
21	chr13:50958800-50959200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr13:50958800-50959800	Enhancers	Primary T cells fromperipheralblood	blood
23	chr13:50958800-50960000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr13:50958800-50960200	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
25	chr13:50958800-50960800	Enhancers	Psoas Muscle	Psoas

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