Variant report

Variant	rs55940904
Chromosome Location	chr5:112342840-112342841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs12521395	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13185006	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17290064	1.00[AMR][1000 genomes]
rs17310536	1.00[AMR][1000 genomes]
rs17311019	1.00[AMR][1000 genomes]
rs17311096	1.00[AMR][1000 genomes]
rs17369211	1.00[AMR][1000 genomes]
rs17369487	1.00[AMR][1000 genomes]
rs17370550	0.89[AMR][1000 genomes]
rs4235775	1.00[EUR][1000 genomes]
rs4235776	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4235780	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4235781	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4235782	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4235783	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4235784	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4235785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4260661	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4276396	1.00[EUR][1000 genomes]
rs4295378	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4519915	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4627978	1.00[EUR][1000 genomes]
rs4705534	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4705535	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4705536	1.00[EUR][1000 genomes]
rs4705757	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4705759	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4705760	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4705761	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4705764	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4705765	1.00[EUR][1000 genomes]
rs55798475	1.00[AMR][1000 genomes]
rs55901036	1.00[AMR][1000 genomes]
rs55997238	0.95[EUR][1000 genomes]
rs56023848	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56265422	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6594657	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6594658	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6594666	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6594667	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6594668	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6862944	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6872473	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6881198	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6881233	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6881426	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6881477	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6882115	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6896675	0.95[EUR][1000 genomes]
rs6897972	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7706745	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7728495	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs878074	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs878075	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	nsv1028759	chr5:112300490-112358514	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv882717	chr5:112336588-112408944	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112314200-112349600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr5:112314200-112356800	Weak transcription	Stomach Mucosa	stomach
3	chr5:112314200-112362600	Weak transcription	Colonic Mucosa	Colon
4	chr5:112314800-112349200	Weak transcription	Brain Substantia Nigra	brain
5	chr5:112315600-112362600	Weak transcription	Brain Angular Gyrus	brain
6	chr5:112317800-112366200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:112318400-112365600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr5:112319800-112363800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr5:112320000-112364200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:112320600-112362600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:112321200-112364800	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr5:112321400-112363800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr5:112321600-112353800	Weak transcription	Fetal Heart	heart
14	chr5:112322600-112362400	Weak transcription	Psoas Muscle	Psoas
15	chr5:112322800-112362400	Weak transcription	Esophagus	oesophagus
16	chr5:112324800-112369800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:112327800-112364600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:112329400-112356800	Strong transcription	Primary B cells from peripheral blood	blood
19	chr5:112330200-112362800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:112332400-112348600	Weak transcription	Brain Hippocampus Middle	brain
21	chr5:112332400-112352400	Strong transcription	Dnd41	blood
22	chr5:112332400-112355800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:112332400-112372600	Weak transcription	Fetal Brain Male	brain
24	chr5:112332600-112349000	Weak transcription	Fetal Brain Female	brain
25	chr5:112332800-112352200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr5:112333000-112349400	Weak transcription	NHLF	lung
27	chr5:112333000-112359800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr5:112333200-112362400	Weak transcription	Right Ventricle	heart
29	chr5:112334000-112365200	Strong transcription	Placenta	Placenta
30	chr5:112334200-112344000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr5:112334200-112350400	Strong transcription	Fetal Intestine Large	intestine
32	chr5:112334200-112350400	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr5:112334200-112352600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr5:112334800-112347600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr5:112334800-112352200	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr5:112335000-112346400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr5:112335200-112343600	Strong transcription	Fetal Stomach	stomach
38	chr5:112335600-112350200	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr5:112335600-112353200	Strong transcription	Fetal Thymus	thymus
40	chr5:112335800-112344000	Strong transcription	Fetal Muscle Trunk	muscle
41	chr5:112335800-112344400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr5:112335800-112350600	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr5:112335800-112351000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr5:112336000-112343800	Strong transcription	Fetal Lung	lung
45	chr5:112336400-112350200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr5:112336400-112350800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr5:112338600-112360800	Weak transcription	Aorta	Aorta
48	chr5:112338800-112345600	Weak transcription	Ovary	ovary
49	chr5:112339000-112349000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr5:112339200-112347800	Weak transcription	Left Ventricle	heart

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