Variant report

Variant	rs2052469
Chromosome Location	chr5:178620316-178620317
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178619900..178622290-chr5:178622494..178625423,2	MCF-7	breast:
2	chr5:178613030..178614553-chr5:178617663..178620440,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10076130	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2052470	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052472	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797608	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3797609	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3822601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4700787	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs4700788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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
19	esv988467	chr5:178613736-178622247	Bivalent Enhancer Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv883229	chr5:178614867-178642524	Enhancers Bivalent Enhancer Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv883230	chr5:178614867-178648369	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv883231	chr5:178614867-178813207	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	nsv984573	chr5:178619213-178643040	ZNF genes & repeats Genic enhancers Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178594800-178627600	Weak transcription	Right Atrium	heart
2	chr5:178607400-178622200	Weak transcription	NHDF-Ad	bronchial
3	chr5:178607400-178636200	Weak transcription	HSMM	muscle
4	chr5:178607600-178626000	Weak transcription	HSMMtube	muscle
5	chr5:178607800-178629000	Weak transcription	NHLF	lung
6	chr5:178608000-178620800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr5:178613600-178623200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:178617400-178621000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr5:178617800-178622400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:178617800-178623000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr5:178618400-178621000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr5:178618400-178622600	Weak transcription	Adipose Nuclei	Adipose
13	chr5:178618800-178623200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:178619000-178622200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:178619000-178625000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:178619000-178635000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:178619200-178620400	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr5:178619200-178623200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:178619400-178620600	Bivalent Enhancer	Fetal Muscle Leg	muscle
20	chr5:178619400-178620800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr5:178619400-178621000	Strong transcription	Osteobl	bone
22	chr5:178619600-178620400	Enhancers	Ovary	ovary
23	chr5:178619600-178620800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:178619600-178622400	Strong transcription	Fetal Stomach	stomach
25	chr5:178619600-178623200	Weak transcription	Fetal Brain Female	brain
26	chr5:178619600-178623400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:178619600-178627200	Weak transcription	Fetal Intestine Small	intestine
28	chr5:178619800-178620600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
29	chr5:178619800-178620800	Genic enhancers	Spleen	Spleen
30	chr5:178619800-178621400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr5:178619800-178622600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:178619800-178650200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:178620000-178620600	Bivalent Enhancer	Brain Cingulate Gyrus	brain
34	chr5:178620000-178620600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
35	chr5:178620000-178621600	Weak transcription	Placenta	Placenta
36	chr5:178620000-178622600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr5:178620200-178620400	Enhancers	Brain Angular Gyrus	brain
38	chr5:178620200-178622600	Weak transcription	Fetal Brain Male	brain
39	chr5:178620200-178622800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr5:178620200-178650200	Weak transcription	Fetal Lung	lung

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