Variant report

Variant	rs9535411
Chromosome Location	chr13:50568872-50568873
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50507293..50510312-chr13:50568081..50571220,3	MCF-7	breast:
2	chr13:50567028..50569486-chr13:50569557..50572350,3	K562	blood:
3	chr13:50568781..50571479-chr13:50962860..50965023,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPRYD7-1	chr13:50567929-50570895	NONHSAT033771

Variant related genes	Relation type
ENSG00000123178	Chromatin interaction
ENSG00000204977	Chromatin interaction
ENSG00000264864	Chromatin interaction
ENSG00000176124	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11839292	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12876820	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1323450	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2066544	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066557	0.83[YRI][hapmap]
rs2066581	0.96[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2066593	0.92[CEU][hapmap];0.98[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]
rs2407884	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2760911	1.00[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs6561570	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7318151	1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9316482	1.00[CEU][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316484	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9526629	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535403	0.87[ASN][1000 genomes]
rs9535407	0.83[YRI][hapmap]
rs9535410	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535414	0.92[CEU][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9535415	0.87[ASN][1000 genomes]
rs9535416	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9568354	0.83[YRI][hapmap]
rs9740075	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9535411	C13orf1	cis	cerebellum	SCAN
rs9535411	TMEM74	trans	parietal	SCAN

Chromatin state (count:75 , 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	chr13:50540400-50569800	Weak transcription	Primary T cells from cord blood	blood
3	chr13:50543600-50570400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:50546000-50569200	Weak transcription	Primary B cells from cord blood	blood
5	chr13:50546000-50570000	Weak transcription	NHLF	lung
6	chr13:50547600-50569800	Weak transcription	Dnd41	blood
7	chr13:50550800-50569600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr13:50550800-50569800	Weak transcription	NH-A	brain
9	chr13:50551000-50569600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr13:50551000-50569600	Weak transcription	Brain Hippocampus Middle	brain
11	chr13:50551000-50569800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr13:50551000-50569800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr13:50551000-50569800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr13:50551000-50570000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr13:50551000-50570200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr13:50551200-50569600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr13:50551400-50570200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr13:50552400-50570200	Weak transcription	Lung	lung
19	chr13:50552800-50569800	Weak transcription	Fetal Lung	lung
20	chr13:50552800-50569800	Weak transcription	Placenta	Placenta
21	chr13:50552800-50570200	Weak transcription	Spleen	Spleen
22	chr13:50553600-50570000	Weak transcription	Left Ventricle	heart
23	chr13:50555000-50569200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr13:50555200-50569600	Weak transcription	Fetal Stomach	stomach
25	chr13:50555200-50569800	Weak transcription	Brain Angular Gyrus	brain
26	chr13:50556800-50570200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr13:50557000-50569800	Weak transcription	Fetal Brain Female	brain
28	chr13:50557200-50570000	Weak transcription	Aorta	Aorta
29	chr13:50558000-50569600	Weak transcription	HUVEC	blood vessel
30	chr13:50558200-50570000	Weak transcription	Esophagus	oesophagus
31	chr13:50558600-50569800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr13:50558600-50569800	Weak transcription	HSMMtube	muscle
33	chr13:50559800-50569800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr13:50560000-50569600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr13:50560000-50570000	Weak transcription	Pancreas	Pancrea
36	chr13:50560200-50569800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr13:50560200-50569800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr13:50560400-50569800	Weak transcription	Brain Anterior Caudate	brain
39	chr13:50561200-50569800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr13:50561200-50570000	Weak transcription	Psoas Muscle	Psoas
41	chr13:50561400-50569800	Weak transcription	Fetal Heart	heart
42	chr13:50562200-50569800	Weak transcription	Brain Substantia Nigra	brain
43	chr13:50562200-50569800	Weak transcription	Fetal Kidney	kidney
44	chr13:50562200-50570000	Weak transcription	Small Intestine	intestine
45	chr13:50562600-50570000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr13:50563000-50569800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr13:50563200-50569000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr13:50563200-50569600	Weak transcription	Thymus	Thymus
49	chr13:50563200-50569800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr13:50563200-50569800	Weak transcription	Fetal Intestine Large	intestine

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