Variant report

Variant	rs11690723
Chromosome Location	chr2:189974104-189974105
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:189969228..189971711-chr2:189972340..189974261,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10178611	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10178886	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10181597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10194682	0.94[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10195184	0.80[ASN][1000 genomes]
rs11686253	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.97[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12622083	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12693526	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12693527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12693528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989558	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13008197	0.94[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.97[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13391332	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13401377	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4667259	0.94[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.97[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6414121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6434310	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6434311	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6434315	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6434316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6434317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6434318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6434321	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6434323	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6738371	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7420511	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7421040	0.94[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7421525	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7423808	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7423973	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7424137	0.83[ASN][1000 genomes]
rs7424790	0.94[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7426169	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7557945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562299	0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7568732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7602447	0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7606293	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[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	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	nsv3074	chr2:189931263-189976124	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189922800-189980800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:189933000-189980200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:189941200-189975000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:189947600-189980800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:189948200-189980600	Weak transcription	Placenta	Placenta
6	chr2:189948600-189974800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:189950800-189977800	Weak transcription	Fetal Intestine Large	intestine
8	chr2:189954800-189980400	Weak transcription	Ovary	ovary
9	chr2:189958200-189981000	Weak transcription	Fetal Stomach	stomach
10	chr2:189960400-189974400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:189962400-189995200	Weak transcription	Aorta	Aorta
12	chr2:189962600-189978800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:189962600-189980600	Weak transcription	Fetal Muscle Leg	muscle
14	chr2:189966400-189974600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:189968600-189977800	Weak transcription	HSMMtube	muscle
16	chr2:189968600-190012000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr2:189969000-189980000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr2:189970200-189974400	Weak transcription	Liver	Liver
19	chr2:189970200-189974800	Weak transcription	Fetal Kidney	kidney
20	chr2:189970200-189974800	Weak transcription	HUVEC	blood vessel
21	chr2:189971000-189978200	Strong transcription	HSMM	muscle
22	chr2:189971400-189976400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:189971600-189974400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:189971600-189977800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:189972000-189974600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:189972200-189975400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:189972600-189974600	Strong transcription	Fetal Lung	lung
28	chr2:189972600-189975600	Strong transcription	NH-A	brain
29	chr2:189972600-189975600	Strong transcription	Osteobl	bone
30	chr2:189972800-189974600	Strong transcription	NHDF-Ad	bronchial
31	chr2:189973000-189975600	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr2:189973000-189980200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:189973400-189974800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:189973400-189974800	Weak transcription	NHLF	lung
35	chr2:189973400-189975200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:189973600-189974200	Strong transcription	A549	lung
37	chr2:189973600-189974800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:189973600-189975000	Strong transcription	Adipose Nuclei	Adipose
39	chr2:189973800-189975200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:189973800-189975200	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:189973800-189975600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links