Variant report

Variant	rs2490638
Chromosome Location	chr13:50568122-50568123
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr13:50567868-50568179	SH-SY5Y	brain:	n/a	n/a
2	GATA3	chr13:50567826-50568133	T-47D	breast:	n/a	n/a
3	GATA3	chr13:50567893-50568136	MCF-7	breast:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:50507293..50510312-chr13:50568081..50571220,3	MCF-7	breast:
2	chr13:50546165..50548667-chr13:50566546..50568183,2	MCF-7	breast:
3	chr13:50561796..50563418-chr13:50566824..50568369,2	MCF-7	breast:
4	chr13:50567028..50569486-chr13:50569557..50572350,3	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPRYD7-1	chr13:50567929-50570895	NONHSAT033771
2	lnc-SPRYD7-1	chr13:50567929-50568127	NONHSAT033781

No data

Variant related genes	Relation type
TRIM13	TF binding region
ENSG00000123178	Chromatin interaction
ENSG00000204977	Chromatin interaction
ENSG00000264864	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs2066550	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2472395	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2476389	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2476391	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2490636	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490637	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2490639	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34047395	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs706609	0.82[EUR][1000 genomes]
rs706615	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs706617	0.82[EUR][1000 genomes]
rs73489867	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs790528	0.82[EUR][1000 genomes]
rs790529	0.82[EUR][1000 genomes]
rs790530	0.82[EUR][1000 genomes]
rs790531	0.82[EUR][1000 genomes]
rs790532	0.82[EUR][1000 genomes]
rs790928	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs790931	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs790934	0.80[EUR][1000 genomes]
rs790935	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs790937	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs790939	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs790940	0.88[ASN][1000 genomes]
rs790941	0.85[AFR][1000 genomes];0.88[ASN][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: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	chr13:50552400-50568800	Weak transcription	GM12878-XiMat	blood
19	chr13:50552400-50570200	Weak transcription	Lung	lung
20	chr13:50552800-50569800	Weak transcription	Fetal Lung	lung
21	chr13:50552800-50569800	Weak transcription	Placenta	Placenta
22	chr13:50552800-50570200	Weak transcription	Spleen	Spleen
23	chr13:50553600-50570000	Weak transcription	Left Ventricle	heart
24	chr13:50555000-50569200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr13:50555200-50569600	Weak transcription	Fetal Stomach	stomach
26	chr13:50555200-50569800	Weak transcription	Brain Angular Gyrus	brain
27	chr13:50556000-50568200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr13:50556800-50570200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr13:50557000-50569800	Weak transcription	Fetal Brain Female	brain
30	chr13:50557200-50570000	Weak transcription	Aorta	Aorta
31	chr13:50557600-50568600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr13:50558000-50569600	Weak transcription	HUVEC	blood vessel
33	chr13:50558200-50570000	Weak transcription	Esophagus	oesophagus
34	chr13:50558600-50569800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr13:50558600-50569800	Weak transcription	HSMMtube	muscle
36	chr13:50559800-50569800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr13:50560000-50569600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr13:50560000-50570000	Weak transcription	Pancreas	Pancrea
39	chr13:50560200-50569800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr13:50560200-50569800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr13:50560400-50569800	Weak transcription	Brain Anterior Caudate	brain
42	chr13:50561000-50568600	Strong transcription	Fetal Thymus	thymus
43	chr13:50561200-50569800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr13:50561200-50570000	Weak transcription	Psoas Muscle	Psoas
45	chr13:50561400-50569800	Weak transcription	Fetal Heart	heart
46	chr13:50562200-50569800	Weak transcription	Brain Substantia Nigra	brain
47	chr13:50562200-50569800	Weak transcription	Fetal Kidney	kidney
48	chr13:50562200-50570000	Weak transcription	Small Intestine	intestine
49	chr13:50562600-50570000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr13:50563000-50569800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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