Variant report

Variant	rs17528473
Chromosome Location	chr5:58559042-58559043
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10036406	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs10038599	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10055446	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs10056754	1.00[LWK][hapmap]
rs10059709	1.00[ASW][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap]
rs10060200	0.81[CEU][hapmap]
rs10061600	0.83[ASN][1000 genomes]
rs10061786	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10062176	1.00[LWK][hapmap]
rs10064893	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.87[ASN][1000 genomes]
rs10068836	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10070294	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070436	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10075364	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10440630	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs11738043	1.00[ASW][hapmap]
rs11740402	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11747413	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs13328160	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13328175	0.91[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13328226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13356883	1.00[ASW][hapmap]
rs13360907	0.98[ASN][1000 genomes]
rs17444059	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17528257	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17528285	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.87[ASN][1000 genomes]
rs17528634	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17724250	0.81[CEU][hapmap]
rs17780213	0.81[CEU][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap]
rs1824159	0.83[CEU][hapmap]
rs2112959	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28529077	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28647633	0.98[ASN][1000 genomes]
rs60453299	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs61683381	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6881054	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72765932	0.87[ASN][1000 genomes]
rs72765942	0.98[ASN][1000 genomes]
rs72765953	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72765961	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72765990	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9292201	0.91[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9292206	1.00[ASW][hapmap]
rs9686434	0.80[AMR][1000 genomes];0.90[EUR][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	nsv598252	chr5:58487764-58618889	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58541600-58560000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr5:58541600-58562400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr5:58541800-58562800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:58552600-58560400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:58553400-58560000	Weak transcription	Fetal Lung	lung
6	chr5:58553800-58568600	Weak transcription	Fetal Muscle Leg	muscle
7	chr5:58554200-58559600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr5:58554200-58561000	Weak transcription	Stomach Mucosa	stomach
9	chr5:58554200-58562600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr5:58557000-58559200	Weak transcription	Hela-S3	cervix
11	chr5:58557200-58560000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:58557200-58560600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr5:58557200-58562400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr5:58557400-58560600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:58558000-58560600	Weak transcription	Fetal Intestine Large	intestine
16	chr5:58558000-58561000	Weak transcription	Fetal Intestine Small	intestine
17	chr5:58558400-58559200	Enhancers	Aorta	Aorta
18	chr5:58558400-58559200	Enhancers	Left Ventricle	heart
19	chr5:58558400-58559200	Enhancers	Pancreas	Pancrea
20	chr5:58558400-58559200	Enhancers	Psoas Muscle	Psoas
21	chr5:58558400-58559200	Enhancers	Right Atrium	heart
22	chr5:58558400-58564400	Enhancers	Fetal Heart	heart
23	chr5:58558600-58559800	Weak transcription	Colon Smooth Muscle	Colon
24	chr5:58558600-58559800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr5:58558600-58560600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr5:58558600-58561000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr5:58558800-58560200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr5:58559000-58559200	Genic enhancers	A549	lung

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