Variant report

Variant	rs17725949
Chromosome Location	chr5:58662920-58662921
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11959801	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11960438	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12186492	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12186633	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs13154145	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs13164719	0.92[EUR][1000 genomes]
rs13189127	0.88[CEU][hapmap]
rs1457145	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1598740	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17726292	0.85[CEU][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17782969	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34433570	0.87[EUR][1000 genomes]
rs34553923	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34756714	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34852844	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62358047	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62358055	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6897015	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7735572	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1030716	chr5:58636116-58718362	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1032732	chr5:58637179-58689010	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1022160	chr5:58645805-58689010	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv881704	chr5:58653383-58675538	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58653000-58669400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:58654400-58667000	Weak transcription	Fetal Intestine Large	intestine
3	chr5:58654600-58665400	Weak transcription	Fetal Muscle Leg	muscle
4	chr5:58654800-58665800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr5:58656200-58665400	Weak transcription	Psoas Muscle	Psoas
6	chr5:58658200-58663400	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr5:58659400-58663400	Weak transcription	Fetal Lung	lung
8	chr5:58659800-58665800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:58659800-58667200	Weak transcription	Fetal Intestine Small	intestine
10	chr5:58660200-58663400	Weak transcription	Brain Substantia Nigra	brain
11	chr5:58660600-58669200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:58661800-58663800	Enhancers	Fetal Heart	heart
13	chr5:58662200-58664000	Enhancers	Rectal Smooth Muscle	rectum
14	chr5:58662400-58663600	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr5:58662600-58663000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr5:58662600-58663000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr5:58662800-58663000	Flanking Active TSS	A549	lung
18	chr5:58662800-58663200	Weak transcription	Colon Smooth Muscle	Colon
19	chr5:58662800-58663800	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr5:58662800-58664000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:58662800-58664000	Enhancers	Hela-S3	cervix

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