Variant report

Variant	rs10863920
Chromosome Location	chr1:211813455-211813456
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRAF5-5	chr1:211813037-211813702	ENSG00000227764
2	lnc-TRAF5-5	chr1:211813314-211814173	NONHSAT009306

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10158305	0.86[EUR][1000 genomes]
rs10158307	0.86[EUR][1000 genomes]
rs10158309	0.86[EUR][1000 genomes]
rs10158749	0.85[EUR][1000 genomes]
rs10158790	0.86[EUR][1000 genomes]
rs10158874	0.85[EUR][1000 genomes]
rs10159253	0.84[EUR][1000 genomes]
rs10779564	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10779565	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10779566	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863919	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119780	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11119783	0.82[EUR][1000 genomes]
rs11119786	0.83[EUR][1000 genomes]
rs11119787	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11576789	0.83[EUR][1000 genomes]
rs11577255	0.83[EUR][1000 genomes]
rs12087826	0.83[EUR][1000 genomes]
rs12090722	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12123429	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12142250	0.85[EUR][1000 genomes]
rs12727505	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12741252	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12758005	0.84[EUR][1000 genomes]
rs1373293	0.86[EUR][1000 genomes]
rs35531215	0.84[EUR][1000 genomes]
rs4245741	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4951415	0.91[ASN][1000 genomes]
rs4951416	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951418	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951419	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951421	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951537	0.84[ASN][1000 genomes]
rs4951539	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951540	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61851777	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540698	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669878	0.86[EUR][1000 genomes]
rs6670986	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671497	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6671506	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682640	0.82[AMR][1000 genomes]
rs6693364	0.82[EUR][1000 genomes]
rs7513348	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7523748	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7551699	0.83[EUR][1000 genomes]
rs894853	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894854	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs894855	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010919	chr1:211804252-211823073	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211804200-211816600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:211807000-211816200	Weak transcription	Colonic Mucosa	Colon
3	chr1:211807000-211816200	Weak transcription	Ovary	ovary
4	chr1:211807200-211816600	Weak transcription	Right Ventricle	heart
5	chr1:211807200-211817200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:211807400-211816800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:211807600-211816600	Weak transcription	Left Ventricle	heart
8	chr1:211810600-211816400	Weak transcription	Spleen	Spleen
9	chr1:211811200-211813600	Enhancers	Placenta	Placenta
10	chr1:211811400-211829600	Enhancers	Fetal Intestine Small	intestine
11	chr1:211811600-211815000	Enhancers	Liver	Liver
12	chr1:211811600-211828200	Enhancers	Fetal Intestine Large	intestine
13	chr1:211811800-211814000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:211812000-211813800	Enhancers	NHDF-Ad	bronchial
15	chr1:211812000-211814000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:211812000-211814400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:211812400-211816600	Weak transcription	Adipose Nuclei	Adipose
18	chr1:211812600-211816600	Weak transcription	Esophagus	oesophagus
19	chr1:211812800-211814000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:211813000-211813600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:211813000-211813600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:211813000-211813600	Flanking Active TSS	HepG2	liver
23	chr1:211813000-211813600	Enhancers	HSMM	muscle
24	chr1:211813000-211813800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:211813000-211813800	Enhancers	Stomach Mucosa	stomach
26	chr1:211813000-211813800	Flanking Active TSS	A549	lung
27	chr1:211813000-211813800	Flanking Active TSS	Osteobl	bone
28	chr1:211813000-211814000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:211813000-211814000	Flanking Active TSS	HUVEC	blood vessel
30	chr1:211813000-211814000	Flanking Active TSS	NH-A	brain
31	chr1:211813000-211814600	Active TSS	Hela-S3	cervix
32	chr1:211813200-211813600	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr1:211813200-211813600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr1:211813200-211813600	Active TSS	Fetal Thymus	thymus
35	chr1:211813200-211814000	Enhancers	Fetal Heart	heart
36	chr1:211813200-211816200	Weak transcription	Pancreas	Pancrea
37	chr1:211813200-211816400	Weak transcription	HMEC	breast
38	chr1:211813200-211816600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:211813200-211817000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:211813400-211813800	Enhancers	H1 Cell Line	embryonic stem cell
41	chr1:211813400-211813800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:211813400-211813800	Flanking Active TSS	NHLF	lung
43	chr1:211813400-211814000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:211813400-211816400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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