Variant report

Variant	rs790928
Chromosome Location	chr13:50679744-50679745
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:50679123..50681390-chr13:50691644..50694719,3	MCF-7	breast:
2	chr13:50679351..50682085-chr13:50688250..50690548,2	K562	blood:
3	chr13:50678670..50682437-chr13:50696050..50699691,4	K562	blood:
4	chr13:50674582..50676260-chr13:50678860..50680465,2	MCF-7	breast:
5	chr13:50678414..50681084-chr13:50693265..50695116,2	MCF-7	breast:
6	chr13:50651347..50654585-chr13:50679189..50682334,3	K562	blood:
7	chr13:50675965..50677737-chr13:50679197..50681160,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNASEH2B-3	chr13:50678840-50681354	NR_002605
2	lnc-RNASEH2B-3	chr13:50678840-50681354	NR_109973

No data

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2066550	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2472395	1.00[AFR][1000 genomes];0.93[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	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2490636	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2490637	0.82[EUR][1000 genomes]
rs2490638	0.90[AFR][1000 genomes];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	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs706609	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs706615	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs706617	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73489867	0.82[EUR][1000 genomes]
rs790528	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs790529	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs790530	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs790531	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs790532	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs790931	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs790934	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs790935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs790937	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs790939	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs790940	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs790941	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][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	nsv832608	chr13:50678628-50888413	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50658000-50697200	Weak transcription	HSMMtube	muscle
2	chr13:50659800-50681600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr13:50659800-50697200	Weak transcription	Hela-S3	cervix
4	chr13:50666400-50680200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr13:50666400-50680400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr13:50666600-50680000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr13:50671600-50689800	Weak transcription	Colonic Mucosa	Colon
8	chr13:50672000-50689400	Weak transcription	Right Ventricle	heart
9	chr13:50673000-50680600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr13:50673000-50695600	Weak transcription	Fetal Intestine Large	intestine
11	chr13:50673200-50682600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr13:50673600-50679800	Weak transcription	Adipose Nuclei	Adipose
13	chr13:50673600-50680200	Weak transcription	Fetal Heart	heart
14	chr13:50673600-50680600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr13:50673600-50681000	Weak transcription	Fetal Lung	lung
16	chr13:50673600-50688400	Weak transcription	HepG2	liver
17	chr13:50673600-50690400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr13:50673800-50680600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr13:50673800-50680600	Weak transcription	Brain Substantia Nigra	brain
20	chr13:50673800-50681000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr13:50673800-50693800	Weak transcription	K562	blood
22	chr13:50673800-50697600	Weak transcription	HSMM	muscle
23	chr13:50674000-50680400	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr13:50674000-50680600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr13:50674000-50680600	Weak transcription	Brain Anterior Caudate	brain
26	chr13:50674000-50680800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr13:50674000-50681400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr13:50674000-50681400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr13:50674000-50681600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr13:50674000-50684800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr13:50674000-50689400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr13:50674000-50689400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr13:50674000-50689600	Weak transcription	Aorta	Aorta
34	chr13:50674000-50693800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr13:50674000-50695000	Weak transcription	Fetal Muscle Leg	muscle
36	chr13:50674000-50695400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr13:50674000-50695600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr13:50674000-50697200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr13:50674000-50697600	Weak transcription	Esophagus	oesophagus
40	chr13:50674200-50680600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr13:50674200-50689400	Weak transcription	Left Ventricle	heart
42	chr13:50674200-50695400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr13:50674600-50680400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr13:50674600-50680600	Weak transcription	Thymus	Thymus
45	chr13:50674600-50695400	Weak transcription	Fetal Intestine Small	intestine
46	chr13:50675000-50680400	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr13:50675000-50680600	Weak transcription	Fetal Thymus	thymus
48	chr13:50676000-50680400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr13:50676800-50681200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr13:50676800-50695800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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