Variant report

Variant	rs11952087
Chromosome Location	chr5:112445471-112445472
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs35555142	0.83[EUR][1000 genomes]
rs4235792	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4259163	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4454046	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4458560	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4527591	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4582268	1.00[EUR][1000 genomes]
rs4705541	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4705781	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60681208	0.83[EUR][1000 genomes]
rs62373350	0.83[EUR][1000 genomes]
rs62373352	0.83[EUR][1000 genomes]
rs62374676	0.83[EUR][1000 genomes]
rs62374682	0.83[EUR][1000 genomes]
rs62374707	0.83[EUR][1000 genomes]
rs62374708	1.00[EUR][1000 genomes]
rs62374709	1.00[EUR][1000 genomes]
rs62374711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6594684	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6594689	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6872711	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73237129	1.00[EUR][1000 genomes]
rs7703001	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1018344	chr5:112390951-112458853	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112384000-112453000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:112424400-112448000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:112426600-112453000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr5:112426800-112450200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:112426800-112450600	Weak transcription	Primary T cells from cord blood	blood
6	chr5:112426800-112450600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr5:112426800-112453800	Weak transcription	HSMMtube	muscle
8	chr5:112427000-112453800	Weak transcription	Fetal Kidney	kidney
9	chr5:112427200-112448200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:112431200-112461600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr5:112432200-112450200	Weak transcription	Spleen	Spleen
12	chr5:112432200-112454600	Weak transcription	Pancreas	Pancrea
13	chr5:112434000-112459200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr5:112437600-112445800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:112437800-112454400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr5:112438000-112450600	Weak transcription	Aorta	Aorta
17	chr5:112438000-112454200	Weak transcription	Psoas Muscle	Psoas
18	chr5:112438200-112450000	Weak transcription	Adipose Nuclei	Adipose
19	chr5:112438200-112450200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:112438200-112452800	Weak transcription	Brain Anterior Caudate	brain
21	chr5:112439600-112454600	Weak transcription	Esophagus	oesophagus
22	chr5:112439800-112452600	Weak transcription	Fetal Lung	lung
23	chr5:112440000-112445600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr5:112440000-112450000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:112440200-112445800	Weak transcription	Ovary	ovary
26	chr5:112440200-112446600	Weak transcription	Right Ventricle	heart
27	chr5:112440200-112447800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:112440200-112447800	Weak transcription	Right Atrium	heart
29	chr5:112440200-112448000	Weak transcription	Fetal Muscle Leg	muscle
30	chr5:112440200-112450000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr5:112440200-112450000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:112440200-112450000	Weak transcription	Fetal Stomach	stomach
33	chr5:112440200-112454200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr5:112440400-112445800	Weak transcription	Fetal Heart	heart
35	chr5:112441600-112447600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:112442400-112446600	Enhancers	Liver	Liver
37	chr5:112442800-112452600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr5:112443400-112448600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr5:112443600-112446400	Weak transcription	Left Ventricle	heart
40	chr5:112444400-112446000	Genic enhancers	NHEK	skin
41	chr5:112444400-112446200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr5:112444400-112446400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr5:112444400-112446800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:112444400-112448600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr5:112444800-112448600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr5:112444800-112450000	Weak transcription	Lung	lung
47	chr5:112445000-112448600	Weak transcription	HMEC	breast

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