Variant report

Variant	rs1862212
Chromosome Location	chr5:178607922-178607923
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178605814..178608090-chr5:178611906..178613466,2	MCF-7	breast:
2	chr5:178606888..178609097-chr5:178620867..178622421,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1106062	0.88[CEU][hapmap];0.84[CHB][hapmap];0.87[EUR][1000 genomes]
rs187539	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs252069	0.84[JPT][hapmap]
rs3797600	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs420251	0.90[EUR][1000 genomes]
rs4701077	0.88[CEU][hapmap];0.84[CHB][hapmap];0.88[EUR][1000 genomes]
rs870311	0.89[CEU][hapmap];0.84[CHB][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs888763	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024560	chr5:178415364-178917595	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv537975	chr5:178415364-178917595	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv1033597	chr5:178423101-178752095	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1031829	chr5:178442633-178658706	Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv482750	chr5:178482653-178663586	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1026790	chr5:178511268-178687428	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv482352	chr5:178525060-178697496	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1016097	chr5:178544084-178866001	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1026968	chr5:178545479-178865895	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv537976	chr5:178545479-178865895	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv600496	chr5:178552518-178752351	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv883223	chr5:178576631-178630445	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv883224	chr5:178604465-178637502	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv883225	chr5:178604465-178639040	Weak transcription Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv883226	chr5:178604465-178645310	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv883227	chr5:178604465-178659691	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv883228	chr5:178604465-178796142	Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178594800-178627600	Weak transcription	Right Atrium	heart
2	chr5:178601600-178609000	Strong transcription	Osteobl	bone
3	chr5:178602000-178608400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:178602200-178609800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:178602800-178612600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:178603200-178608200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr5:178603400-178608000	Strong transcription	Muscle Satellite Cultured Cells	--
8	chr5:178603400-178614200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr5:178606000-178609800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:178606600-178608000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:178606600-178608200	Strong transcription	Adipose Nuclei	Adipose
12	chr5:178606600-178608400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:178607000-178608200	Strong transcription	Ovary	ovary
14	chr5:178607000-178615200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr5:178607400-178608000	Weak transcription	Aorta	Aorta
16	chr5:178607400-178608200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr5:178607400-178608400	Genic enhancers	Fetal Lung	lung
18	chr5:178607400-178614400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:178607400-178622200	Weak transcription	NHDF-Ad	bronchial
20	chr5:178607400-178636200	Weak transcription	HSMM	muscle
21	chr5:178607600-178608000	Bivalent Enhancer	HepG2	liver
22	chr5:178607600-178608200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:178607600-178609000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:178607600-178626000	Weak transcription	HSMMtube	muscle
25	chr5:178607800-178608000	Enhancers	Fetal Muscle Trunk	muscle
26	chr5:178607800-178609200	Weak transcription	Spleen	Spleen
27	chr5:178607800-178609400	Strong transcription	Fetal Stomach	stomach
28	chr5:178607800-178611000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:178607800-178612400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr5:178607800-178629000	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links