Variant report

Variant	rs73081825
Chromosome Location	chr3:56603863-56603864
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:56595109..56597404-chr3:56602239..56604027,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10049468	0.81[AMR][1000 genomes]
rs11130537	0.88[ASN][1000 genomes]
rs17235670	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2317134	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2317244	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2317252	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs282522	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs282523	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs282528	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs282536	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs282541	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4234393	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4681933	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4681945	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4681980	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4681994	0.82[ASN][1000 genomes]
rs4682000	0.82[ASN][1000 genomes]
rs55831745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55938093	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56190096	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56204053	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6445801	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6445803	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6445804	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6445810	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6778373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781056	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781293	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6787227	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6792321	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6809499	0.88[ASN][1000 genomes]
rs73079883	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73079884	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73079891	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73079902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73081810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73081811	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73081819	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73081823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73081851	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73081854	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7617331	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7619465	0.81[AMR][1000 genomes]
rs7620259	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7631662	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7637449	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7642389	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9809309	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9833926	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9835332	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9839065	0.82[ASN][1000 genomes]
rs9858568	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9875257	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9878373	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347557	chr3:56466500-56619322	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv460557	chr3:56594735-56661320	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv590362	chr3:56594735-56661320	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	esv3338042	chr3:56602712-56606910	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv2555353	chr3:56603725-56605249	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	esv3404626	chr3:56603737-56606285	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs73081825	CCDC66	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56592000-56615600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:56592200-56609400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:56592400-56607400	Weak transcription	Psoas Muscle	Psoas
4	chr3:56592400-56615600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
6	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
7	chr3:56592800-56610200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:56592800-56644600	Weak transcription	Fetal Heart	heart
9	chr3:56593000-56607800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:56593000-56610000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:56593200-56608000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:56593200-56609000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:56593200-56609600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:56593200-56616400	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:56593400-56607600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:56593400-56608600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:56593600-56609800	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr3:56594200-56608000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:56594200-56610200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:56594400-56609400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:56594800-56604000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr3:56594800-56609000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:56596000-56605800	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr3:56596000-56608400	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:56597200-56609200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:56597400-56609400	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:56597400-56610000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:56597600-56605400	Strong transcription	Hela-S3	cervix
29	chr3:56597600-56608000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:56597800-56607600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:56598000-56607000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:56598000-56607800	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr3:56598000-56609200	Strong transcription	Fetal Thymus	thymus
34	chr3:56598000-56609800	Strong transcription	Primary T cells from cord blood	blood
35	chr3:56598600-56608400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:56598600-56609600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr3:56598800-56607600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr3:56599600-56606000	Strong transcription	Thymus	Thymus
39	chr3:56599600-56606200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr3:56599800-56606000	Strong transcription	Fetal Stomach	stomach
41	chr3:56599800-56606200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:56599800-56607800	Strong transcription	Fetal Lung	lung
43	chr3:56599800-56608000	Strong transcription	Liver	Liver
44	chr3:56600000-56604000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:56600000-56604000	Strong transcription	NHEK	skin
46	chr3:56600000-56604200	Strong transcription	Colonic Mucosa	Colon
47	chr3:56600000-56604400	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:56600000-56606000	Strong transcription	Fetal Intestine Small	intestine
49	chr3:56600000-56606600	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:56600000-56606800	Strong transcription	Osteobl	bone

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