Variant report

Variant	rs4262539
Chromosome Location	chr1:158985652-158985653
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11539423	0.88[AMR][1000 genomes]
rs12728586	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12734915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12738378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12739704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12755219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1361564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1361565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16841500	0.88[AMR][1000 genomes]
rs1956	0.88[AMR][1000 genomes]
rs66519738	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72704976	0.88[AMR][1000 genomes]
rs7526724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs856047	0.85[AMR][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	esv3376764	chr1:158761947-158998617	Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv3369957	chr1:158915589-159003393	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv3176	chr1:158955373-158986568	Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv872486	chr1:158979191-159090256	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158976000-159000800	Weak transcription	Gastric	stomach
2	chr1:158977200-158990400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:158978800-158985800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr1:158980200-159025400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:158981200-158986400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:158981600-158986000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr1:158982000-158988000	Weak transcription	Fetal Brain Male	brain
8	chr1:158982600-158986200	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:158982600-159027400	Weak transcription	Fetal Kidney	kidney
10	chr1:158982800-158987800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:158982800-158989600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:158982800-159000200	Weak transcription	Aorta	Aorta
13	chr1:158983000-158986000	Genic enhancers	Osteobl	bone
14	chr1:158983000-158987200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:158983200-158986000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:158983400-158985800	Enhancers	Small Intestine	intestine
17	chr1:158983400-158987200	Transcr. at gene 5' and 3'	Dnd41	blood
18	chr1:158983600-158987200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
19	chr1:158983600-158988000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr1:158983800-158986000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:158983800-158986000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:158984000-158986000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
23	chr1:158984000-158986200	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:158984000-158986400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:158984000-158986600	Genic enhancers	HSMMtube	muscle
26	chr1:158984000-158988000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:158984000-158991600	Strong transcription	Fetal Lung	lung
28	chr1:158984000-159000800	Weak transcription	Right Ventricle	heart
29	chr1:158984200-158985800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr1:158984200-158986000	Genic enhancers	NHEK	skin
31	chr1:158984200-158987200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:158984200-158991400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr1:158984200-159024200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:158984400-158986000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
35	chr1:158984400-158986600	Genic enhancers	Fetal Thymus	thymus
36	chr1:158984400-158987200	Genic enhancers	Hela-S3	cervix
37	chr1:158984400-158995200	Strong transcription	Fetal Intestine Large	intestine
38	chr1:158984600-158986200	Genic enhancers	NHLF	lung
39	chr1:158984600-158987200	Genic enhancers	Spleen	Spleen
40	chr1:158984800-158986000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:158984800-158986000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:158984800-158986000	Genic enhancers	HMEC	breast
43	chr1:158984800-158986000	Genic enhancers	HSMM	muscle
44	chr1:158984800-158986800	Strong transcription	Fetal Muscle Leg	muscle
45	chr1:158984800-159027400	Weak transcription	Psoas Muscle	Psoas
46	chr1:158985000-158985800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:158985200-158985800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
48	chr1:158985200-158985800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells	blood
49	chr1:158985200-158986000	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
50	chr1:158985200-158986000	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links