Variant report

Variant	rs790939
Chromosome Location	chr13:50660881-50660882
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50652169..50667024-chr13:50693268..50703943,57	K562	blood:
2	chr13:50653006..50665770-chr13:50696335..50703879,43	K562	blood:
3	chr13:50654073..50663597-chr13:50696674..50702768,25	MCF-7	breast:
4	chr13:50652189..50666968-chr13:50693462..50701392,46	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231607	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs2066550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2472395	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2476389	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2476391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2490636	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2490637	0.82[EUR][1000 genomes]
rs2490638	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2490639	0.82[EUR][1000 genomes]
rs2687933	0.82[EUR][1000 genomes]
rs2687934	0.82[EUR][1000 genomes]
rs2687935	0.82[EUR][1000 genomes]
rs2687936	0.82[EUR][1000 genomes]
rs2812223	0.82[EUR][1000 genomes]
rs34047395	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs706609	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs706615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs706617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73489867	0.82[EUR][1000 genomes]
rs790528	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs790529	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs790530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs790531	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs790532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs790928	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs790931	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs790934	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs790935	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs790937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs790940	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs790941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[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:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50657200-50665000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr13:50657200-50673400	Weak transcription	Pancreas	Pancrea
3	chr13:50657400-50673400	Weak transcription	Left Ventricle	heart
4	chr13:50657400-50673400	Weak transcription	HSMM	muscle
5	chr13:50658000-50673400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr13:50658000-50697200	Weak transcription	HSMMtube	muscle
7	chr13:50658200-50665800	Weak transcription	Fetal Intestine Small	intestine
8	chr13:50658400-50665800	Weak transcription	Psoas Muscle	Psoas
9	chr13:50658400-50673400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr13:50658600-50673400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr13:50659200-50661400	Genic enhancers	Primary B cells from cord blood	blood
12	chr13:50659200-50666000	Weak transcription	GM12878-XiMat	blood
13	chr13:50659400-50666000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr13:50659400-50666000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr13:50659600-50662000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr13:50659600-50665000	Weak transcription	Brain Hippocampus Middle	brain
17	chr13:50659600-50665200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr13:50659600-50665800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr13:50659600-50665800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr13:50659600-50666000	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr13:50659600-50672600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr13:50659600-50673000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr13:50659600-50673200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr13:50659800-50661000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr13:50659800-50661000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr13:50659800-50662200	Weak transcription	NHLF	lung
27	chr13:50659800-50664800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr13:50659800-50664800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr13:50659800-50665000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr13:50659800-50665000	Weak transcription	Brain Germinal Matrix	brain
31	chr13:50659800-50665200	Weak transcription	Fetal Heart	heart
32	chr13:50659800-50665400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr13:50659800-50665600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr13:50659800-50666000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr13:50659800-50666200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr13:50659800-50666200	Weak transcription	Adipose Nuclei	Adipose
37	chr13:50659800-50666600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr13:50659800-50668600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr13:50659800-50669000	Weak transcription	NHDF-Ad	bronchial
40	chr13:50659800-50670800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr13:50659800-50671200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr13:50659800-50671600	Weak transcription	HMEC	breast
43	chr13:50659800-50672200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr13:50659800-50672400	Weak transcription	A549	lung
45	chr13:50659800-50672600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr13:50659800-50672600	Weak transcription	Fetal Lung	lung
47	chr13:50659800-50672600	Weak transcription	Osteobl	bone
48	chr13:50659800-50673400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr13:50659800-50673400	Weak transcription	NH-A	brain
50	chr13:50659800-50681600	Weak transcription	Brain Cingulate Gyrus	brain

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