Variant report

Variant	rs6802498
Chromosome Location	chr3:56723660-56723661
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	chr3:56715854..56718511-chr3:56721135..56727135,8	MCF-7	breast:
2	chr3:56715900..56719627-chr3:56722769..56727051,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163946	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10049468	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11130537	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11130540	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11130541	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1565373	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1565375	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1844477	0.81[AMR][1000 genomes]
rs2317134	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2317244	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2317252	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs282522	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs282523	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs282528	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs282536	0.85[ASN][1000 genomes]
rs282541	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4234393	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4681725	0.80[EUR][1000 genomes]
rs4681734	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4681740	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4681933	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4681945	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4681964	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4681980	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4681994	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682000	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55938093	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs56190096	0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs56204053	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs62251242	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6445801	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6445803	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6445804	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6445810	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6445814	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6773823	0.81[AMR][1000 genomes]
rs6773931	0.81[AMR][1000 genomes]
rs6787227	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6809499	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73081851	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs73081854	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7617331	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7618007	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7619465	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7620259	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7631662	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7637449	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7642389	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9311614	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9809309	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9833926	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9835332	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9839065	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9851653	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9858568	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9875257	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9878373	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6802498	CCDC66	cis	Thyroid	GTEx
rs6802498	ARHGEF3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56717600-56725200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:56717600-56725200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:56717800-56725200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:56717800-56725200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:56717800-56726800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:56718000-56725200	Weak transcription	Dnd41	blood
7	chr3:56718000-56725200	Weak transcription	HMEC	breast
8	chr3:56718000-56727000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:56718000-56727400	Weak transcription	HSMMtube	muscle
10	chr3:56718200-56725000	Weak transcription	Placenta	Placenta
11	chr3:56718400-56727000	Weak transcription	HSMM	muscle
12	chr3:56718800-56726600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:56719000-56725800	Weak transcription	Fetal Thymus	thymus
14	chr3:56721400-56724000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:56722400-56726600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr3:56722400-56727000	Weak transcription	Primary B cells from cord blood	blood
17	chr3:56722600-56725200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:56722600-56726800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr3:56722800-56725200	Weak transcription	NHEK	skin
20	chr3:56723400-56724200	Enhancers	HepG2	liver
21	chr3:56723600-56727000	Weak transcription	GM12878-XiMat	blood

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