Variant report

Variant	rs9535410
Chromosome Location	chr13:50561473-50561474
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50560599..50562822-chr13:50654339..50656712,2	MCF-7	breast:
2	chr13:50558774..50566292-chr13:50567433..50571184,7	K562	blood:
3	chr13:50558774..50562499-chr13:50568042..50570799,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPRYD7-1	chr13:50550469-50565502	NONHSAT033771
2	lnc-TRIM13-2	chr13:50560539-50561585	NONHSAT033779

Variant related genes	Relation type
ENSG00000264864	Chromatin interaction
ENSG00000176124	Chromatin interaction
ENSG00000231607	Chromatin interaction
ENSG00000204977	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11839292	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12876820	0.87[ASN][1000 genomes]
rs1323450	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2066544	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066581	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2407884	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561570	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7318151	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9316482	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316484	0.87[ASN][1000 genomes]
rs9526629	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535403	0.87[ASN][1000 genomes]
rs9535411	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535414	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9535415	0.87[ASN][1000 genomes]
rs9535416	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9740075	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][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	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

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50539000-50570000	Weak transcription	Fetal Intestine Small	intestine
2	chr13:50540200-50562200	Weak transcription	Adipose Nuclei	Adipose
3	chr13:50540400-50569800	Weak transcription	Primary T cells from cord blood	blood
4	chr13:50543600-50570400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr13:50545800-50562000	Weak transcription	Fetal Intestine Large	intestine
6	chr13:50546000-50569200	Weak transcription	Primary B cells from cord blood	blood
7	chr13:50546000-50570000	Weak transcription	NHLF	lung
8	chr13:50547600-50561800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr13:50547600-50569800	Weak transcription	Dnd41	blood
10	chr13:50550800-50562200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr13:50550800-50569600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr13:50550800-50569800	Weak transcription	NH-A	brain
13	chr13:50551000-50562000	Weak transcription	HSMM	muscle
14	chr13:50551000-50562800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr13:50551000-50569600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr13:50551000-50569600	Weak transcription	Brain Hippocampus Middle	brain
17	chr13:50551000-50569800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr13:50551000-50569800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr13:50551000-50569800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr13:50551000-50570000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr13:50551000-50570200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr13:50551200-50562200	Weak transcription	NHDF-Ad	bronchial
23	chr13:50551200-50569600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr13:50551400-50570200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr13:50552400-50568800	Weak transcription	GM12878-XiMat	blood
26	chr13:50552400-50570200	Weak transcription	Lung	lung
27	chr13:50552800-50569800	Weak transcription	Fetal Lung	lung
28	chr13:50552800-50569800	Weak transcription	Placenta	Placenta
29	chr13:50552800-50570200	Weak transcription	Spleen	Spleen
30	chr13:50553600-50570000	Weak transcription	Left Ventricle	heart
31	chr13:50555000-50562800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr13:50555000-50569200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr13:50555200-50565800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr13:50555200-50569600	Weak transcription	Fetal Stomach	stomach
35	chr13:50555200-50569800	Weak transcription	Brain Angular Gyrus	brain
36	chr13:50556000-50568200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr13:50556800-50570200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr13:50557000-50569800	Weak transcription	Fetal Brain Female	brain
39	chr13:50557200-50570000	Weak transcription	Aorta	Aorta
40	chr13:50557600-50565200	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr13:50557600-50568600	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr13:50558000-50566200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr13:50558000-50569600	Weak transcription	HUVEC	blood vessel
44	chr13:50558200-50570000	Weak transcription	Esophagus	oesophagus
45	chr13:50558600-50561800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr13:50558600-50566800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr13:50558600-50569800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr13:50558600-50569800	Weak transcription	HSMMtube	muscle
49	chr13:50558800-50561800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr13:50558800-50562200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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