Variant report

Variant	rs2880055
Chromosome Location	chr1:161922365-161922366
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:161920696..161923597-chr16:85495262..85497654,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10733044	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737502	0.90[ASN][1000 genomes]
rs10753645	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10753666	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800068	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1394070	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1553444	0.94[ASN][1000 genomes]
rs1806594	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055539	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2134690	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2134696	0.90[ASN][1000 genomes]
rs2298019	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2341468	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2341479	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2499855	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2499856	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34312480	1.00[ASN][1000 genomes]
rs34461550	0.90[ASN][1000 genomes]
rs35621393	0.94[ASN][1000 genomes]
rs36080602	1.00[ASN][1000 genomes]
rs3767633	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4233380	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300199	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4579731	0.90[ASN][1000 genomes]
rs4656335	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4656339	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657103	0.90[ASN][1000 genomes]
rs6427633	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427639	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667896	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6685369	0.90[ASN][1000 genomes]
rs6698065	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701754	0.90[ASN][1000 genomes]
rs71639910	0.98[ASN][1000 genomes]
rs7517386	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532448	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs924777	0.81[AMR][1000 genomes];0.90[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	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv464206	chr1:161798239-162067447	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv470744	chr1:161798239-162067447	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv548077	chr1:161798239-162067447	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161824200-161928400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:161861600-161936000	Weak transcription	Fetal Intestine Small	intestine
3	chr1:161883400-161928200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:161884600-161927600	Weak transcription	NHEK	skin
5	chr1:161884800-161922600	Weak transcription	Brain Anterior Caudate	brain
6	chr1:161885000-161928000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr1:161887000-161928200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:161887200-161929600	Weak transcription	Hela-S3	cervix
9	chr1:161897800-161928400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:161897800-161940000	Weak transcription	Brain Germinal Matrix	brain
11	chr1:161901400-161935400	Weak transcription	Fetal Lung	lung
12	chr1:161902400-161923000	Weak transcription	Brain Substantia Nigra	brain
13	chr1:161902800-161943400	Weak transcription	Esophagus	oesophagus
14	chr1:161903600-161930400	Weak transcription	Fetal Brain Female	brain
15	chr1:161903800-161923800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:161904400-161923200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:161904800-161956600	Weak transcription	Fetal Brain Male	brain
18	chr1:161906000-161923200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:161906000-161923200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:161906000-161927800	Weak transcription	Thymus	Thymus
21	chr1:161906800-161923200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr1:161906800-161928000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:161906800-161932200	Weak transcription	Stomach Mucosa	stomach
24	chr1:161907000-161923200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:161910600-161922600	Weak transcription	Brain Angular Gyrus	brain
26	chr1:161911000-161937200	Weak transcription	Gastric	stomach
27	chr1:161911600-161923800	Weak transcription	Small Intestine	intestine
28	chr1:161911600-161939400	Weak transcription	HepG2	liver
29	chr1:161912400-161923400	Weak transcription	Fetal Thymus	thymus
30	chr1:161912600-161923400	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr1:161912600-161941600	Weak transcription	Fetal Kidney	kidney
32	chr1:161912800-161927800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:161913600-161928000	Weak transcription	Fetal Intestine Large	intestine
34	chr1:161913600-161931600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:161914000-161932000	Weak transcription	Aorta	Aorta
36	chr1:161914600-161925600	Weak transcription	Right Ventricle	heart
37	chr1:161914600-161927800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr1:161914600-161927800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr1:161914800-161923200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:161914800-161923400	Weak transcription	Dnd41	blood
41	chr1:161914800-161925400	Weak transcription	Left Ventricle	heart
42	chr1:161914800-161928000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:161914800-161928000	Weak transcription	Placenta	Placenta
44	chr1:161915000-161922800	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr1:161915000-161923000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr1:161915000-161925000	Weak transcription	Liver	Liver
47	chr1:161915000-161928400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:161915000-161930800	Weak transcription	HUVEC	blood vessel
49	chr1:161915200-161922400	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr1:161915200-161923800	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links