Variant report

Variant	rs13012649
Chromosome Location	chr2:190009066-190009067
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	chr2:190008421..190011287-chr2:190151088..190152689,2	MCF-7	breast:
2	chr2:190007864..190009528-chr2:190088531..190091177,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10931400	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10931404	0.84[EUR][1000 genomes]
rs11681286	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12104769	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12105389	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12611950	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12615823	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12618438	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12621035	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12621806	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12621939	0.87[EUR][1000 genomes]
rs12991770	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12993719	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12995956	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12999122	0.89[EUR][1000 genomes]
rs12999996	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13004722	0.80[EUR][1000 genomes]
rs13005652	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13005821	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13011374	0.82[EUR][1000 genomes]
rs13011485	0.81[EUR][1000 genomes]
rs13012327	0.84[EUR][1000 genomes]
rs13015283	0.89[EUR][1000 genomes]
rs13016231	0.89[EUR][1000 genomes]
rs13017413	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13019076	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13021508	0.81[EUR][1000 genomes]
rs13022633	0.83[EUR][1000 genomes]
rs13028967	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13029705	0.97[EUR][1000 genomes]
rs13031211	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13031549	0.84[EUR][1000 genomes]
rs13033421	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1356162	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1356163	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1356164	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1356165	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1356167	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1356168	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1399991	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1399992	0.84[EUR][1000 genomes]
rs1515874	0.84[EUR][1000 genomes]
rs1515876	0.84[EUR][1000 genomes]
rs1568334	0.81[EUR][1000 genomes]
rs1878085	0.90[EUR][1000 genomes]
rs1949484	0.89[EUR][1000 genomes]
rs1965422	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2138374	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2222256	0.89[EUR][1000 genomes]
rs2351627	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2351636	0.80[EUR][1000 genomes]
rs35475196	0.84[EUR][1000 genomes]
rs3914778	0.89[EUR][1000 genomes]
rs4233801	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4428040	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4667264	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4667265	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4667272	0.89[EUR][1000 genomes]
rs4667274	0.85[EUR][1000 genomes]
rs4667276	0.81[EUR][1000 genomes]
rs4667277	0.81[EUR][1000 genomes]
rs4998559	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60124911	0.90[EUR][1000 genomes]
rs62182416	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6434339	0.80[EUR][1000 genomes]
rs6708419	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6714088	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6719104	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6737071	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7419888	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7561002	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7564611	0.83[EUR][1000 genomes]
rs7576165	0.82[EUR][1000 genomes]
rs7587147	0.89[EUR][1000 genomes]
rs7587956	0.89[EUR][1000 genomes]
rs7607133	0.85[EUR][1000 genomes]
rs7609495	0.84[EUR][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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189968600-190012000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr2:189981400-190014800	Weak transcription	Fetal Stomach	stomach
3	chr2:189984000-190016800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:189993800-190017000	Weak transcription	Ovary	ovary
5	chr2:189994200-190010600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:189999000-190009400	Weak transcription	Fetal Muscle Leg	muscle
7	chr2:190000400-190013600	Weak transcription	Left Ventricle	heart
8	chr2:190003600-190014600	Weak transcription	Colon Smooth Muscle	Colon
9	chr2:190006600-190011800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:190007400-190009200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:190007800-190009600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:190007800-190010600	Strong transcription	HSMM	muscle
13	chr2:190008000-190009200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:190008000-190010000	Enhancers	Fetal Lung	lung
15	chr2:190008000-190014800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:190008400-190009400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:190008400-190009800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:190008600-190009200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:190008600-190009800	Strong transcription	NH-A	brain
20	chr2:190008800-190009200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:190008800-190009200	Flanking Active TSS	NHDF-Ad	bronchial
22	chr2:190008800-190009600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:190008800-190009600	Enhancers	Aorta	Aorta
24	chr2:190008800-190009600	Enhancers	Osteobl	bone
25	chr2:190008800-190009800	Enhancers	NHLF	lung
26	chr2:190008800-190010000	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr2:190009000-190009200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr2:190009000-190009200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:190009000-190009800	Genic enhancers	Muscle Satellite Cultured Cells	--
30	chr2:190009000-190009800	Enhancers	Adipose Nuclei	Adipose
31	chr2:190009000-190010200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr2:190009000-190011400	Weak transcription	HSMMtube	muscle
33	chr2:190009000-190012000	Enhancers	A549	lung
34	chr2:190009000-190016000	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