Variant report

Variant	rs58887996
Chromosome Location	chr5:178569941-178569942
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10076252	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12187962	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2278221	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2278222	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2303638	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34132209	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34346845	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34447103	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34865831	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35311590	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35718962	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35814218	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35926292	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3776817	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41285551	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7729756	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv883222	chr5:178540975-178595870	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	nsv600495	chr5:178547567-178570914	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178548600-178570000	Weak transcription	NHDF-Ad	bronchial
2	chr5:178549400-178590800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr5:178551600-178582800	Weak transcription	Right Atrium	heart
4	chr5:178554000-178587800	Weak transcription	Colonic Mucosa	Colon
5	chr5:178557000-178585400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr5:178560200-178578400	Weak transcription	Aorta	Aorta
7	chr5:178563000-178570200	Weak transcription	NHLF	lung
8	chr5:178563200-178579000	Weak transcription	Fetal Lung	lung
9	chr5:178565200-178582600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:178565400-178570000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:178565400-178570600	Weak transcription	Lung	lung
12	chr5:178565600-178575800	Weak transcription	Spleen	Spleen
13	chr5:178565600-178579400	Weak transcription	Ovary	ovary
14	chr5:178567000-178594000	Weak transcription	Gastric	stomach
15	chr5:178567200-178581000	Weak transcription	Fetal Muscle Leg	muscle
16	chr5:178567400-178574600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr5:178567400-178575000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr5:178567400-178575400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr5:178568600-178570800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:178568800-178575200	Weak transcription	Fetal Stomach	stomach
21	chr5:178569000-178570200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:178569000-178570800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:178569200-178570800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr5:178569400-178570400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr5:178569400-178570600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:178569400-178570600	Enhancers	Placenta Amnion	Placenta Amnion
27	chr5:178569400-178570800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:178569400-178570800	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr5:178569400-178571600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr5:178569600-178570000	Enhancers	Dnd41	blood
31	chr5:178569600-178570200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr5:178569600-178570200	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr5:178569600-178570600	Enhancers	Adipose Nuclei	Adipose
34	chr5:178569600-178570800	Enhancers	Muscle Satellite Cultured Cells	--
35	chr5:178569600-178570800	Enhancers	HSMM	muscle
36	chr5:178569600-178570800	Enhancers	HSMMtube	muscle
37	chr5:178569600-178571800	Enhancers	Osteobl	bone
38	chr5:178569800-178570800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:178569800-178573400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr5:178569800-178573400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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