Variant report

Variant	rs11960587
Chromosome Location	chr5:60608162-60608163
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:60607093..60609330-chr5:60616167..60617939,2	MCF-7	breast:
2	chr5:60607732..60609238-chr5:60626633..60628648,2	MCF-7	breast:
3	chr5:60457106..60459969-chr5:60606928..60608823,2	MCF-7	breast:
4	chr5:60596572..60599250-chr5:60605731..60609279,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130449	Chromatin interaction
ENSG00000188725	Chromatin interaction
ENSG00000251279	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10041973	0.83[ASN][1000 genomes]
rs10939894	0.80[ASN][1000 genomes]
rs10939895	0.82[ASN][1000 genomes]
rs10939897	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs10939898	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11743133	0.91[EUR][1000 genomes]
rs11747144	0.85[CEU][hapmap];0.98[EUR][1000 genomes]
rs11949390	0.80[ASN][1000 genomes]
rs12696982	0.82[ASN][1000 genomes]
rs13154581	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13154663	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs13156118	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13162866	0.86[CEU][hapmap];0.98[EUR][1000 genomes]
rs13164720	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs13171223	0.88[EUR][1000 genomes]
rs13174916	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs13178686	0.92[CEU][hapmap]
rs13179814	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13182603	0.88[EUR][1000 genomes]
rs34027100	0.80[ASN][1000 genomes]
rs34323293	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4315878	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4409043	0.94[EUR][1000 genomes]
rs4513641	0.86[CEU][hapmap];0.94[EUR][1000 genomes]
rs4544785	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs4640746	0.82[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs62366231	0.83[ASN][1000 genomes]
rs62366236	0.94[EUR][1000 genomes]
rs6449523	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6449526	0.81[CEU][hapmap]
rs6870349	0.93[CEU][hapmap];0.98[EUR][1000 genomes]
rs6881622	0.97[EUR][1000 genomes]
rs72759299	0.82[ASN][1000 genomes]
rs7704636	0.94[EUR][1000 genomes]
rs7721603	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[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	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv823089	chr5:60589501-60669903	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60600600-60609800	Weak transcription	Ovary	ovary
2	chr5:60600800-60615800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:60602800-60608200	Weak transcription	HMEC	breast
4	chr5:60603000-60608200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:60603200-60609800	Weak transcription	Fetal Lung	lung
6	chr5:60603200-60609800	Weak transcription	Stomach Mucosa	stomach
7	chr5:60603800-60608200	Weak transcription	NHEK	skin
8	chr5:60603800-60609200	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr5:60603800-60609600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:60605200-60609800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:60605200-60609800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:60606600-60610400	Enhancers	Placenta	Placenta
13	chr5:60606600-60610800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:60606600-60611200	Enhancers	Hela-S3	cervix
15	chr5:60606600-60611400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:60606600-60611800	Enhancers	HSMM	muscle
17	chr5:60606800-60608800	Enhancers	Stomach Smooth Muscle	stomach
18	chr5:60607200-60608400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:60607200-60610200	Enhancers	Muscle Satellite Cultured Cells	--
20	chr5:60607200-60610200	Enhancers	HUVEC	blood vessel
21	chr5:60607200-60611800	Enhancers	NHLF	lung
22	chr5:60607400-60608400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:60607400-60608800	Enhancers	Colon Smooth Muscle	Colon
24	chr5:60607400-60609800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr5:60607400-60610200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr5:60607600-60609400	Weak transcription	Lung	lung
27	chr5:60607600-60609800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr5:60607600-60610600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:60607600-60611400	Enhancers	Osteobl	bone
30	chr5:60607800-60608800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr5:60607800-60608800	Flanking Active TSS	A549	lung
32	chr5:60607800-60609800	Enhancers	HSMMtube	muscle
33	chr5:60607800-60611400	Enhancers	NHDF-Ad	bronchial
34	chr5:60607800-60611800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:60607800-60614600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:60608000-60608800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:60608000-60608800	Enhancers	Rectal Smooth Muscle	rectum
38	chr5:60608000-60609000	Enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links