Variant report

Variant	rs16878597
Chromosome Location	chr5:80610388-80610389
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80603897..80608830-chr5:80609104..80612341,4	K562	blood:

Variant related genes	Relation type
ENSG00000131732	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10514218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10942946	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739833	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11739834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11740916	1.00[ASN][1000 genomes]
rs11743842	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11743849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11745275	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749113	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11953113	0.96[EUR][1000 genomes]
rs11957137	0.96[EUR][1000 genomes]
rs12516089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12517538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12518716	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12523578	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16878594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56067803	1.00[ASN][1000 genomes]
rs62365025	0.83[EUR][1000 genomes]
rs62365031	1.00[ASN][1000 genomes]
rs62365032	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62365035	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62365038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62365866	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62365867	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72771170	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7731320	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs16878597	CTC-281B15.1	cis	Nerve Tibial	GTEx
rs16878597	CTC-281B15.1	cis	Stomach	GTEx
rs16878597	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs16878597	CTC-281B15.1	cis	Esophagus Mucosa	GTEx
rs16878597	CTC-281B15.1	cis	Thyroid	GTEx
rs16878597	CTC-281B15.1	cis	Artery Tibial	GTEx
rs16878597	CTC-281B15.1	cis	Adipose Subcutaneous	GTEx
rs16878597	CTC-281B15.1	cis	lung	GTEx
rs16878597	CTC-281B15.1	cis	Skin Sun Exposed Lower leg	GTEx
rs16878597	CTC-281B15.1	cis	Artery Aorta	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80598200-80612400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:80598400-80611200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:80598600-80611200	Weak transcription	Brain Anterior Caudate	brain
4	chr5:80598600-80611200	Weak transcription	Fetal Brain Male	brain
5	chr5:80598600-80611200	Weak transcription	Small Intestine	intestine
6	chr5:80598600-80611200	Weak transcription	Stomach Mucosa	stomach
7	chr5:80598600-80611800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:80598800-80611000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr5:80598800-80611200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:80599200-80612200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:80599400-80610400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:80599600-80610600	Weak transcription	Fetal Heart	heart
13	chr5:80599600-80611200	Weak transcription	Brain Substantia Nigra	brain
14	chr5:80599800-80611400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:80601400-80611000	Weak transcription	Hela-S3	cervix
16	chr5:80601400-80612400	Weak transcription	Colon Smooth Muscle	Colon
17	chr5:80601400-80612400	Weak transcription	Thymus	Thymus
18	chr5:80601600-80611000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:80601600-80611200	Weak transcription	Colonic Mucosa	Colon
20	chr5:80601600-80611200	Weak transcription	Spleen	Spleen
21	chr5:80601600-80611600	Weak transcription	Esophagus	oesophagus
22	chr5:80604200-80611200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr5:80604200-80611400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr5:80604200-80611600	Strong transcription	Primary T cells from cord blood	blood
25	chr5:80604400-80610400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:80604400-80610600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr5:80604400-80610600	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr5:80604400-80610600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr5:80604400-80610600	Strong transcription	Dnd41	blood
30	chr5:80604400-80610800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr5:80604400-80611000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr5:80604400-80611200	Strong transcription	Fetal Thymus	thymus
33	chr5:80604800-80610600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr5:80604800-80610800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr5:80604800-80611000	Strong transcription	Fetal Muscle Trunk	muscle
36	chr5:80604800-80611400	Strong transcription	Primary B cells from cord blood	blood
37	chr5:80605000-80610600	Strong transcription	Placenta	Placenta
38	chr5:80605000-80610800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr5:80605200-80610600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:80605200-80610800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:80605400-80610800	Strong transcription	Adipose Nuclei	Adipose
42	chr5:80606200-80610400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr5:80606400-80610400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr5:80606400-80610800	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr5:80606800-80611800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr5:80607000-80611600	Weak transcription	Brain Angular Gyrus	brain
47	chr5:80607000-80612400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr5:80607000-80612800	Weak transcription	Fetal Intestine Small	intestine
49	chr5:80607200-80611200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr5:80607200-80611200	Weak transcription	Right Ventricle	heart

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