Variant report

Variant	rs233131
Chromosome Location	chr1:85795259-85795260
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	chr1:85783416..85785101-chr1:85792646..85795360,2	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1001604	0.83[EUR][1000 genomes]
rs10489513	0.83[EUR][1000 genomes]
rs11161607	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11161610	0.84[ASN][1000 genomes]
rs11161611	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12044537	0.86[EUR][1000 genomes]
rs12047422	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12124170	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12125557	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12140103	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1498373	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1498375	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1554597	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs173026	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs18582	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884139	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2011825	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2012683	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2177461	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2207368	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2268667	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2300634	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2300637	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs233047	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233050	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs233053	0.86[EUR][1000 genomes]
rs233054	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233055	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs233057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233060	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233061	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs233062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233066	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233067	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233068	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs233069	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233071	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233072	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs233074	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233091	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233093	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233095	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs233097	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs233099	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233108	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233109	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs233112	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs233113	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233114	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233115	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233118	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs233119	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233120	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233121	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233124	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs233127	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233133	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2892888	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3087894	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768227	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3949301	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs423105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949890	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4949900	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6576763	0.84[EUR][1000 genomes]
rs6576764	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6576765	0.83[EUR][1000 genomes]
rs6576767	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6657817	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6671599	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66811655	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6704103	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67611930	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72724606	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs761601	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997251	0.91[EUR][1000 genomes];0.89[ASN][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	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85780000-85795800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr1:85780200-85795800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr1:85780400-85795800	Weak transcription	Gastric	stomach
4	chr1:85783000-85795800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:85783200-85795800	Weak transcription	Aorta	Aorta
6	chr1:85788600-85797400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:85789400-85795800	Weak transcription	Liver	Liver
8	chr1:85789800-85795800	Weak transcription	Fetal Stomach	stomach
9	chr1:85789800-85795800	Weak transcription	Lung	lung
10	chr1:85790000-85795600	Enhancers	NHDF-Ad	bronchial
11	chr1:85790400-85795600	Weak transcription	Brain Germinal Matrix	brain
12	chr1:85790400-85796200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr1:85790400-85797000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:85790600-85800000	Enhancers	HUVEC	blood vessel
15	chr1:85791000-85796800	Enhancers	HepG2	liver
16	chr1:85791200-85798000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:85791400-85797400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:85792000-85795400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:85792000-85795800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:85792200-85795600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr1:85792200-85796400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr1:85792200-85806000	Weak transcription	Fetal Kidney	kidney
23	chr1:85792400-85796200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:85792600-85795600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:85792600-85797800	Weak transcription	Fetal Intestine Small	intestine
26	chr1:85792800-85796600	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr1:85793000-85797000	Enhancers	HMEC	breast
28	chr1:85793200-85797000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:85793200-85797600	Enhancers	NHEK	skin
30	chr1:85793200-85798600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:85793400-85797600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:85793600-85795800	Enhancers	Muscle Satellite Cultured Cells	--
33	chr1:85793600-85795800	Weak transcription	Colon Smooth Muscle	Colon
34	chr1:85793600-85798200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:85793800-85795800	Enhancers	NHLF	lung
36	chr1:85794000-85796600	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr1:85794000-85797000	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr1:85794000-85798200	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr1:85794200-85795600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:85794200-85795600	Enhancers	NH-A	brain
41	chr1:85794200-85795800	Enhancers	HSMM	muscle
42	chr1:85794200-85796600	Enhancers	Placenta	Placenta
43	chr1:85794200-85798000	Enhancers	Fetal Muscle Leg	muscle
44	chr1:85794400-85795800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:85794400-85795800	Enhancers	Osteobl	bone
46	chr1:85794400-85796200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:85794400-85796800	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr1:85794400-85797400	Enhancers	Fetal Heart	heart
49	chr1:85794600-85795600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:85794600-85795800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links