Variant report

Variant	rs2339954
Chromosome Location	chr10:53992507-53992508
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10824262	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10824291	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10824295	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10824300	0.86[EUR][1000 genomes]
rs10824303	0.86[EUR][1000 genomes]
rs11001241	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11001339	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11001343	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11001447	0.80[EUR][1000 genomes]
rs1194505	0.90[ASN][1000 genomes]
rs12218397	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12768182	0.86[EUR][1000 genomes]
rs1875792	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1875794	0.89[EUR][1000 genomes]
rs1919460	0.80[EUR][1000 genomes]
rs1919461	0.80[EUR][1000 genomes]
rs1919462	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4041235	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7074246	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7083967	0.80[EUR][1000 genomes]
rs7907681	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045692	chr10:53301450-54086823	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2750961	chr10:53726294-54010594	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv532194	chr10:53746620-54735550	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv895399	chr10:53900872-54219820	Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2621844	chr10:53982660-54033949	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv5974	chr10:53984049-54034016	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv3377297	chr10:53984068-54034061	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv3359737	chr10:53984078-54034047	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv3361575	chr10:53984134-54034048	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv3494769	chr10:53984145-54034011	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv3494770	chr10:53984145-54034011	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv3378490	chr10:53984169-54034027	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	esv3376659	chr10:53984202-54033986	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	esv3072	chr10:53984224-54034020	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	esv3371586	chr10:53984271-54033985	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv982876	chr10:53989312-53999791	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	lncRNA	n/a	inside rSNPs	n/a

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:53990800-53993000	Enhancers	Primary B cells from peripheral blood	blood
2	chr10:53991600-53992600	Enhancers	Primary B cells from cord blood	blood
3	chr10:53991800-53992600	Enhancers	Primary hematopoietic stem cells	blood
4	chr10:53991800-53993000	Enhancers	GM12878-XiMat	blood
5	chr10:53991800-53993200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr10:53992000-53992800	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr10:53992200-53992600	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr10:53992200-53992600	Enhancers	HUVEC	blood vessel
9	chr10:53992200-53992800	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr10:53992200-53992800	Enhancers	Stomach Mucosa	stomach
11	chr10:53992400-53992600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr10:53992400-53992600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
13	chr10:53992400-53992600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr10:53992400-53992600	Enhancers	Fetal Intestine Small	intestine
15	chr10:53992400-53992600	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr10:53992400-53992600	Enhancers	Hela-S3	cervix
17	chr10:53992400-53992600	Enhancers	HMEC	breast
18	chr10:53992400-53992600	Enhancers	NHEK	skin
19	chr10:53992400-53992800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr10:53992400-53992800	Enhancers	H1 Cell Line	embryonic stem cell
21	chr10:53992400-53992800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr10:53992400-53992800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr10:53992400-53992800	Enhancers	Primary T cells from cord blood	blood
24	chr10:53992400-53992800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr10:53992400-53992800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr10:53992400-53992800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr10:53992400-53992800	Enhancers	Fetal Intestine Large	intestine
28	chr10:53992400-53992800	Enhancers	Fetal Thymus	thymus
29	chr10:53992400-53992800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr10:53992400-53992800	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr10:53992400-53992800	Enhancers	Thymus	Thymus
32	chr10:53992400-53992800	Enhancers	HepG2	liver
33	chr10:53992400-53992800	Enhancers	HSMM	muscle
34	chr10:53992400-53992800	Enhancers	NHLF	lung
35	chr10:53992400-53993000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr10:53992400-53993000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr10:53992400-53993000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr10:53992400-53993000	Enhancers	Adipose Nuclei	Adipose
39	chr10:53992400-53993000	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr10:53992400-53993000	Flanking Active TSS	Fetal Lung	lung
41	chr10:53992400-53993000	Flanking Active TSS	A549	lung
42	chr10:53992400-53993200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr10:53992400-53993200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr10:53992400-53993200	Enhancers	NH-A	brain

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