Variant report

Variant	rs1189425
Chromosome Location	chr13:95782192-95782193
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:95753163..95755993-chr13:95781109..95783183,3	MCF-7	breast:
2	chr13:95752693..95755831-chr13:95780565..95782684,3	MCF-7	breast:
3	chr13:95767278..95770224-chr13:95779723..95782766,3	MCF-7	breast:
4	chr13:95779479..95782281-chr13:95805249..95807826,2	MCF-7	breast:
5	chr13:95780970..95784135-chr13:95784777..95787622,4	K562	blood:
6	chr13:95773275..95777718-chr13:95779226..95784336,7	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1189423	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1189424	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1189427	0.86[ASN][1000 genomes]
rs1189428	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1189429	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1564353	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1564354	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1564355	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1618485	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1678342	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1678371	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1678394	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1729742	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1729748	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1729751	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1729761	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1751064	0.83[ASN][1000 genomes]
rs2127295	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2127296	0.81[EUR][1000 genomes]
rs2478464	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2619314	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2698243	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2766481	0.86[EUR][1000 genomes]
rs3782956	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3825415	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5023599	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[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	nsv533659	chr13:95757713-96042149	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv832689	chr13:95759073-95921308	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95727000-95791600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr13:95727000-95812000	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr13:95731200-95791600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr13:95740800-95791200	Weak transcription	NHLF	lung
5	chr13:95750400-95812400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr13:95750400-95815400	Weak transcription	Fetal Intestine Large	intestine
7	chr13:95751000-95793400	Weak transcription	Fetal Kidney	kidney
8	chr13:95751600-95795600	Weak transcription	Small Intestine	intestine
9	chr13:95752000-95789000	Weak transcription	Aorta	Aorta
10	chr13:95752200-95823200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr13:95752200-95844200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr13:95754000-95794800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr13:95754400-95782600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr13:95756400-95828200	Weak transcription	HSMM	muscle
15	chr13:95757600-95814400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr13:95758000-95791600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr13:95761400-95789200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr13:95762200-95817200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr13:95762400-95811800	Weak transcription	K562	blood
20	chr13:95768200-95783400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr13:95768200-95806600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr13:95768200-95819000	Weak transcription	Fetal Intestine Small	intestine
23	chr13:95769000-95789400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr13:95769400-95791200	Weak transcription	Esophagus	oesophagus
25	chr13:95769800-95789000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr13:95770200-95789200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr13:95774200-95784000	Enhancers	Stomach Mucosa	stomach
28	chr13:95774400-95788800	Weak transcription	GM12878-XiMat	blood
29	chr13:95774400-95788800	Weak transcription	NHEK	skin
30	chr13:95774600-95791200	Weak transcription	Primary T cells from cord blood	blood
31	chr13:95774600-95815800	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr13:95776600-95789400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr13:95776800-95785600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr13:95776800-95789400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr13:95778600-95791800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr13:95778800-95799200	Weak transcription	Colon Smooth Muscle	Colon
37	chr13:95778800-95833400	Weak transcription	Spleen	Spleen
38	chr13:95780000-95782400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr13:95780200-95785800	Weak transcription	Lung	lung
40	chr13:95780800-95791200	Weak transcription	Gastric	stomach
41	chr13:95781000-95791200	Weak transcription	Pancreas	Pancrea
42	chr13:95781000-95792200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr13:95781000-95802400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr13:95781400-95782600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr13:95781400-95782600	Weak transcription	Fetal Lung	lung
46	chr13:95781600-95791200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr13:95781800-95782600	Enhancers	A549	lung
48	chr13:95782000-95828000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links