Variant report

Variant	rs6445801
Chromosome Location	chr3:56649594-56649595
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:56649188-56649638	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:56648967-56664047	K562	blood:	n/a	n/a
3	FOS	chr3:56649395-56649664	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
CCDC66	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10049468	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11130537	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17235670	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2317134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2317244	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2317252	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs282522	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282523	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs282528	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs282536	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282541	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234393	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4681734	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4681740	0.82[EUR][1000 genomes]
rs4681933	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681945	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681964	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4681980	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4681994	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4682000	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55831745	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55938093	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56190096	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56204053	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62251242	0.82[EUR][1000 genomes]
rs6445803	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445804	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445809	0.82[AMR][1000 genomes]
rs6445810	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6445814	0.81[EUR][1000 genomes]
rs6778373	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6781056	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6781293	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6787227	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6792321	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6802498	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6809499	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73079883	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs73079884	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs73079891	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs73079902	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73081810	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73081811	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73081819	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73081823	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73081825	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73081851	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73081854	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617331	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618007	0.80[EUR][1000 genomes]
rs7619465	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7620259	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631662	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7637449	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642389	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9809309	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9833926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835332	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839065	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9851653	0.81[EUR][1000 genomes]
rs9858568	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9875257	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9878373	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[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	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
2	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
3	nsv820061	chr3:56648862-56650174	Strong transcription Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6445801	CCDC66	cis	Thyroid	GTEx
rs6445801	ARHGEF3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56603200-56650400	Weak transcription	K562	blood
2	chr3:56606200-56650200	Weak transcription	Colonic Mucosa	Colon
3	chr3:56607800-56650200	Weak transcription	Psoas Muscle	Psoas
4	chr3:56625200-56650400	Weak transcription	NHEK	skin
5	chr3:56625200-56653400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:56626400-56656200	Weak transcription	Stomach Mucosa	stomach
7	chr3:56628600-56649600	Weak transcription	HepG2	liver
8	chr3:56630000-56654400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:56634000-56651400	Weak transcription	Fetal Brain Male	brain
10	chr3:56640000-56650000	Weak transcription	HMEC	breast
11	chr3:56640400-56650800	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:56640600-56650400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:56640600-56652600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:56640800-56649800	Weak transcription	Fetal Kidney	kidney
15	chr3:56640800-56650400	Weak transcription	NHLF	lung
16	chr3:56640800-56650600	Weak transcription	HSMMtube	muscle
17	chr3:56640800-56650800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:56640800-56664200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:56640800-56695400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:56642800-56713400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:56644200-56664000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:56644400-56652000	Strong transcription	Fetal Lung	lung
23	chr3:56644400-56686400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:56644600-56655800	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:56644600-56665600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:56644600-56668600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:56644800-56649600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:56644800-56649600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr3:56644800-56655400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:56644800-56656000	Strong transcription	Fetal Muscle Leg	muscle
31	chr3:56644800-56669800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:56644800-56708200	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr3:56645000-56650600	Weak transcription	A549	lung
34	chr3:56645000-56650800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr3:56645200-56651600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:56645200-56657000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr3:56645400-56653800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:56645400-56667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:56645400-56705200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr3:56645600-56650600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:56645600-56653400	Weak transcription	Fetal Heart	heart
42	chr3:56645600-56656000	Strong transcription	Fetal Intestine Large	intestine
43	chr3:56645600-56656000	Strong transcription	Fetal Muscle Trunk	muscle
44	chr3:56645600-56664800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:56645600-56665800	Strong transcription	Hela-S3	cervix
46	chr3:56645800-56662000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr3:56645800-56663800	Strong transcription	HSMM	muscle
48	chr3:56646000-56662800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:56646200-56659200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:56646600-56650600	Weak transcription	Left Ventricle	heart

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