Variant report

Variant	rs298624
Chromosome Location	chr5:60476874-60476875
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10044518	1.00[JPT][hapmap]
rs10044575	1.00[JPT][hapmap]
rs12186613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188621	1.00[JPT][hapmap]
rs12188882	1.00[JPT][hapmap]
rs159373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159379	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159540	0.88[ASN][1000 genomes]
rs167190	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1841504	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545476	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2613632	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295523	1.00[CEU][hapmap];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]
rs295525	1.00[CEU][hapmap];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]
rs295526	1.00[CEU][hapmap];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]
rs295529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295538	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs295547	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295548	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295549	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295550	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs295568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295570	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295572	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295574	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295576	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295577	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295581	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4256302	1.00[JPT][hapmap]
rs498497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603018	1.00[CEU][hapmap];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]

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	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60468600-60484400	Weak transcription	Aorta	Aorta
2	chr5:60476400-60477200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:60476400-60477200	Active TSS	NHLF	lung
4	chr5:60476400-60477400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr5:60476600-60477000	Active TSS	Primary hematopoietic stem cells	blood
6	chr5:60476600-60477000	Active TSS	Monocytes-CD14+_RO01746	blood
7	chr5:60476600-60477200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:60476600-60477200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:60476600-60477200	Active TSS	Muscle Satellite Cultured Cells	--
10	chr5:60476600-60477200	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr5:60476600-60477200	Active TSS	Fetal Lung	lung
12	chr5:60476600-60477200	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr5:60476600-60477200	Active TSS	Right Atrium	heart
14	chr5:60476600-60477200	Flanking Active TSS	Dnd41	blood
15	chr5:60476600-60477200	Active TSS	GM12878-XiMat	blood
16	chr5:60476600-60477200	Active TSS	HUVEC	blood vessel
17	chr5:60476600-60477400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:60476600-60477400	Active TSS	A549	lung
19	chr5:60476600-60477600	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr5:60476800-60477000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
21	chr5:60476800-60477200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:60476800-60477200	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr5:60476800-60477200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr5:60476800-60477200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:60476800-60477200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:60476800-60477200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:60476800-60477200	Active TSS	Duodenum Mucosa	Duodenum
28	chr5:60476800-60477200	Active TSS	Rectal Smooth Muscle	rectum
29	chr5:60476800-60477200	Active TSS	Stomach Smooth Muscle	stomach
30	chr5:60476800-60477200	Active TSS	Thymus	Thymus
31	chr5:60476800-60477200	Active TSS	K562	blood
32	chr5:60476800-60477200	Active TSS	NH-A	brain
33	chr5:60476800-60477200	Active TSS	NHDF-Ad	bronchial
34	chr5:60476800-60477200	Active TSS	NHEK	skin
35	chr5:60476800-60477200	Active TSS	Osteobl	bone
36	chr5:60476800-60477400	Active TSS	Adipose Nuclei	Adipose
37	chr5:60476800-60478400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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