Variant report

Variant	rs17780213
Chromosome Location	chr5:58591013-58591014
allele	C/T
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:42)

rs_ID	r²[population]
rs10036406	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs10038599	0.81[CEU][hapmap]
rs10055446	0.88[CEU][hapmap]
rs10056754	1.00[LWK][hapmap]
rs10059709	1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs10060200	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs10061786	0.80[CEU][hapmap]
rs10062176	1.00[LWK][hapmap]
rs10064893	1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs10070294	0.81[CEU][hapmap]
rs10070436	0.84[EUR][1000 genomes]
rs10079396	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10079614	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10079932	0.85[EUR][1000 genomes]
rs11740402	1.00[MEX][hapmap];0.87[TSI][hapmap]
rs11747413	0.83[AMR][1000 genomes]
rs13328160	0.81[CEU][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap]
rs13328175	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13328226	0.81[CEU][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap]
rs13354210	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs17444059	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[LWK][hapmap]
rs17528285	0.89[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes]
rs17528473	0.81[CEU][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap]
rs17528634	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17724250	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17780584	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs17780740	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs17780836	1.00[JPT][hapmap]
rs1824159	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs2044419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112959	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs2194210	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs56183128	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57516309	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60453299	0.84[EUR][1000 genomes]
rs61683381	1.00[ASN][1000 genomes]
rs72765990	1.00[ASN][1000 genomes]
rs72765993	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767722	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9292201	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9686434	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1030117	chr5:58587672-58637179	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58583600-58592400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:58583600-58592600	Weak transcription	Psoas Muscle	Psoas
3	chr5:58583600-58596400	Weak transcription	Esophagus	oesophagus
4	chr5:58583800-58591200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:58584000-58591800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:58584000-58596400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:58584800-58592400	Weak transcription	Fetal Intestine Large	intestine
8	chr5:58587800-58592800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:58588000-58592400	Weak transcription	Brain Hippocampus Middle	brain
10	chr5:58588200-58591200	Weak transcription	Fetal Heart	heart
11	chr5:58588400-58591400	Genic enhancers	A549	lung
12	chr5:58588600-58592400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:58588600-58592400	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr5:58588800-58592200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:58588800-58592400	Enhancers	Hela-S3	cervix
16	chr5:58589000-58592400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr5:58589000-58592400	Enhancers	Colon Smooth Muscle	Colon
18	chr5:58589400-58591400	Enhancers	Rectal Smooth Muscle	rectum
19	chr5:58589600-58591400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr5:58589600-58591800	Enhancers	Stomach Smooth Muscle	stomach
21	chr5:58589800-58591200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:58589800-58591400	Weak transcription	HUVEC	blood vessel
23	chr5:58589800-58592000	Weak transcription	NHEK	skin
24	chr5:58589800-58592400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr5:58589800-58592600	Weak transcription	Left Ventricle	heart
26	chr5:58590000-58591600	Weak transcription	HMEC	breast
27	chr5:58590200-58591800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:58590200-58592200	Weak transcription	Stomach Mucosa	stomach
29	chr5:58590200-58592400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:58590200-58594800	Weak transcription	Gastric	stomach
31	chr5:58590400-58592400	Weak transcription	Right Atrium	heart
32	chr5:58590600-58592800	Weak transcription	Fetal Stomach	stomach
33	chr5:58590800-58591200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr5:58591000-58591600	Enhancers	Skeletal Muscle Female	skeletal muscle

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