Variant report

Variant	rs17128025
Chromosome Location	chr1:86117320-86117321
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	chr1:86114750..86117708-chr1:86118928..86121953,3	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs17127904	1.00[AFR][1000 genomes]
rs17127933	1.00[AFR][1000 genomes]
rs17127978	1.00[AFR][1000 genomes]
rs17127983	1.00[AFR][1000 genomes]
rs17127986	1.00[AFR][1000 genomes]
rs17127994	1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs17128015	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17128031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17128041	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17128046	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17128058	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17128059	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17128061	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17128070	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17128074	0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17128075	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17128078	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17128084	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17128098	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17128109	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17128114	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17128165	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17128173	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17128176	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17128181	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17128216	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17128220	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17128234	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17128240	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17128242	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17128243	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17128249	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17128271	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17128273	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17128279	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17128284	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17128287	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17128290	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17128302	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17395346	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6672587	1.00[AFR][1000 genomes]
rs9658588	1.00[AFR][1000 genomes]
rs9658592	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86094000-86118600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr1:86095400-86119000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:86095400-86134800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:86102800-86118200	Weak transcription	K562	blood
5	chr1:86103400-86173000	Weak transcription	Pancreas	Pancrea
6	chr1:86103600-86117800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:86103600-86119000	Weak transcription	Spleen	Spleen
8	chr1:86103600-86119400	Weak transcription	Fetal Heart	heart
9	chr1:86103600-86119800	Weak transcription	NHLF	lung
10	chr1:86103600-86120200	Weak transcription	HMEC	breast
11	chr1:86103600-86141200	Weak transcription	Thymus	Thymus
12	chr1:86103600-86142200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:86103600-86145400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:86103600-86145600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:86103600-86157400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:86103600-86172600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:86103600-86172600	Weak transcription	Gastric	stomach
18	chr1:86104600-86117800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:86105000-86118000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr1:86105200-86118000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:86105200-86118800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:86105200-86119000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:86106000-86141200	Weak transcription	Lung	lung
24	chr1:86108000-86118800	Weak transcription	Colonic Mucosa	Colon
25	chr1:86113000-86119000	Weak transcription	Fetal Brain Male	brain
26	chr1:86113200-86118400	Weak transcription	Hela-S3	cervix
27	chr1:86113200-86119000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:86114000-86118800	Weak transcription	HSMMtube	muscle
29	chr1:86114000-86119000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr1:86114000-86119200	Weak transcription	HepG2	liver
31	chr1:86114000-86141200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr1:86114000-86143600	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:86114200-86118200	Weak transcription	Osteobl	bone
34	chr1:86114200-86118600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:86114200-86118600	Weak transcription	Fetal Lung	lung
36	chr1:86114200-86120200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:86114400-86117400	Weak transcription	Fetal Thymus	thymus
38	chr1:86114400-86118600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr1:86114400-86119600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:86114400-86142200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr1:86114400-86163200	Weak transcription	Esophagus	oesophagus
42	chr1:86114600-86118000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:86114600-86119000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:86114600-86119000	Weak transcription	Fetal Intestine Small	intestine
45	chr1:86114800-86117800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr1:86115000-86119000	Weak transcription	Fetal Muscle Leg	muscle
47	chr1:86115000-86119000	Weak transcription	NHEK	skin
48	chr1:86115000-86119800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:86115200-86117400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:86115200-86118200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links