Variant report

Variant	rs1560088
Chromosome Location	chr5:16686359-16686360
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10060275	0.94[ASN][1000 genomes]
rs10060411	0.95[ASN][1000 genomes]
rs11738070	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11740825	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11741866	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1560087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1863996	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2288432	0.96[ASN][1000 genomes]
rs2288433	0.96[ASN][1000 genomes]
rs2288434	0.96[ASN][1000 genomes]
rs2288435	0.96[ASN][1000 genomes]
rs2288436	0.96[ASN][1000 genomes]
rs2288437	0.96[ASN][1000 genomes]
rs2303703	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2401987	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs256929	0.84[EUR][1000 genomes]
rs256930	0.84[EUR][1000 genomes]
rs256935	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs257047	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs257049	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs257050	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs257051	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs257198	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs26745	0.88[ASN][1000 genomes]
rs26746	0.91[ASN][1000 genomes]
rs26748	0.92[ASN][1000 genomes]
rs26749	0.92[ASN][1000 genomes]
rs26750	0.94[ASN][1000 genomes]
rs26757	0.94[ASN][1000 genomes]
rs26758	0.96[ASN][1000 genomes]
rs27350	0.90[ASN][1000 genomes]
rs27501	0.94[ASN][1000 genomes]
rs27553	0.88[ASN][1000 genomes]
rs27880	0.90[ASN][1000 genomes]
rs28056	0.90[ASN][1000 genomes]
rs28057	0.90[ASN][1000 genomes]
rs31579	0.81[EUR][1000 genomes]
rs399833	0.96[ASN][1000 genomes]
rs4701670	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4702166	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58619409	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59574363	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6860226	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6881621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6889243	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7717840	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7733988	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7735007	0.94[ASN][1000 genomes]
rs890911	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869660	chr5:16651289-16766428	Genic enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv4737	chr5:16681166-16707357	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16661600-16689400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:16661800-16700000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:16663000-16712400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:16663600-16695400	Strong transcription	Fetal Intestine Small	intestine
5	chr5:16663800-16690800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr5:16663800-16694400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:16663800-16698000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:16663800-16702400	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr5:16663800-16713400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:16664000-16701000	Strong transcription	Fetal Intestine Large	intestine
11	chr5:16664000-16702000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:16664000-16702200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr5:16664000-16702400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:16664200-16702200	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:16664600-16690600	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr5:16665600-16699200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:16667800-16701000	Weak transcription	Right Ventricle	heart
18	chr5:16671000-16691000	Strong transcription	Fetal Muscle Trunk	muscle
19	chr5:16671200-16690200	Strong transcription	HUVEC	blood vessel
20	chr5:16673800-16713400	Weak transcription	Psoas Muscle	Psoas
21	chr5:16674200-16687000	Strong transcription	Fetal Lung	lung
22	chr5:16674200-16693000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:16675000-16690400	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr5:16675800-16713600	Weak transcription	Left Ventricle	heart
25	chr5:16677600-16690200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr5:16677800-16690800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:16677800-16706000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:16678000-16691000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:16678000-16691400	Strong transcription	Duodenum Mucosa	Duodenum
30	chr5:16678200-16687600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:16678200-16690200	Strong transcription	HepG2	liver
32	chr5:16678200-16690800	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr5:16678200-16691000	Strong transcription	Fetal Muscle Leg	muscle
34	chr5:16678200-16691000	Strong transcription	NH-A	brain
35	chr5:16678200-16691200	Strong transcription	A549	lung
36	chr5:16678400-16690000	Strong transcription	Brain Anterior Caudate	brain
37	chr5:16678400-16690000	Strong transcription	Brain Hippocampus Middle	brain
38	chr5:16678400-16690200	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr5:16678400-16690600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr5:16678400-16691000	Strong transcription	Lung	lung
41	chr5:16678600-16686400	Strong transcription	HSMMtube	muscle
42	chr5:16678600-16691000	Strong transcription	HMEC	breast
43	chr5:16678600-16695000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr5:16678800-16686600	Strong transcription	Placenta	Placenta
45	chr5:16678800-16690200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
46	chr5:16678800-16690200	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr5:16679200-16688600	Strong transcription	NHDF-Ad	bronchial
48	chr5:16679600-16693200	Weak transcription	Esophagus	oesophagus
49	chr5:16679600-16701000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr5:16680200-16695000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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