Variant report

Variant	rs877744
Chromosome Location	chr5:59062470-59062471
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10514856	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10940647	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10940648	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11741470	1.00[CEU][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs11747378	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs13164391	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13168643	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs13177163	1.00[CEU][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13186779	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs159612	1.00[CHD][hapmap];0.85[TSI][hapmap]
rs159614	1.00[CHD][hapmap];0.86[TSI][hapmap]
rs17742447	0.81[TSI][hapmap]
rs2938781	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs2938782	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs2938787	0.85[CEU][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs2963820	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs2963823	0.95[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs298056	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs298069	0.89[CEU][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs298087	0.83[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs298101	0.81[TSI][hapmap]
rs3111174	1.00[CHD][hapmap]
rs35302677	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35339176	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35526661	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59251157	0.88[EUR][1000 genomes]
rs62370530	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7709094	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv427720	chr5:58913581-59086987	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59048800-59064000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:59052600-59064200	Weak transcription	Aorta	Aorta
3	chr5:59055800-59063600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:59060800-59065200	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr5:59061400-59062800	Enhancers	Fetal Brain Male	brain
6	chr5:59061400-59063000	Flanking Active TSS	HUVEC	blood vessel
7	chr5:59061400-59064400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:59061400-59065200	Active TSS	Fetal Brain Female	brain
9	chr5:59061600-59063400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:59061600-59065000	Active TSS	Colon Smooth Muscle	Colon
11	chr5:59061600-59065200	Active TSS	Rectal Smooth Muscle	rectum
12	chr5:59061600-59065200	Active TSS	A549	lung
13	chr5:59061800-59063800	Active TSS	Brain Germinal Matrix	brain
14	chr5:59061800-59065600	Active TSS	Hela-S3	cervix
15	chr5:59062000-59062600	Enhancers	Esophagus	oesophagus
16	chr5:59062000-59062600	Enhancers	Small Intestine	intestine
17	chr5:59062000-59062800	Flanking Active TSS	Fetal Lung	lung
18	chr5:59062000-59063000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:59062000-59063000	Enhancers	Stomach Mucosa	stomach
20	chr5:59062000-59063400	Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr5:59062000-59063800	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:59062000-59063800	Flanking Active TSS	NHEK	skin
23	chr5:59062000-59064800	Active TSS	Fetal Stomach	stomach
24	chr5:59062000-59065200	Active TSS	Placenta Amnion	Placenta Amnion
25	chr5:59062000-59065400	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr5:59062200-59062600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr5:59062200-59062600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:59062200-59062600	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr5:59062200-59062600	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr5:59062200-59062600	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr5:59062200-59062600	Flanking Active TSS	Fetal Muscle Leg	muscle
32	chr5:59062200-59062600	Enhancers	Right Ventricle	heart
33	chr5:59062200-59062600	Flanking Active TSS	Stomach Smooth Muscle	stomach
34	chr5:59062200-59062800	Enhancers	Fetal Intestine Large	intestine
35	chr5:59062200-59063000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:59062200-59063000	Flanking Active TSS	Fetal Intestine Small	intestine
37	chr5:59062200-59063000	Flanking Active TSS	HMEC	breast
38	chr5:59062200-59063000	Enhancers	HSMM	muscle
39	chr5:59062200-59063000	Flanking Active TSS	NH-A	brain
40	chr5:59062200-59063600	Enhancers	Fetal Heart	heart
41	chr5:59062200-59064000	Active TSS	Brain Anterior Caudate	brain
42	chr5:59062200-59064000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr5:59062200-59064000	Active TSS	Rectal Mucosa Donor 31	rectum
44	chr5:59062200-59065000	Active TSS	Colonic Mucosa	Colon
45	chr5:59062200-59065000	Active TSS	Fetal Kidney	kidney
46	chr5:59062200-59065200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr5:59062200-59065200	Active TSS	Right Atrium	heart
48	chr5:59062400-59062600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr5:59062400-59062600	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr5:59062400-59062600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose

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