Variant report

Variant	rs7620896
Chromosome Location	chr3:56723125-56723126
allele	A/G
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: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10222629	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1054092	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1054093	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130525	0.82[EUR][1000 genomes]
rs11130526	0.82[EUR][1000 genomes]
rs11130527	0.86[EUR][1000 genomes]
rs11130542	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11712664	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11712799	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11719707	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11719726	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1316647	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13317989	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1388256	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1565378	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1812347	0.86[EUR][1000 genomes]
rs1873256	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2291498	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2291500	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2317132	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs282525	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs282530	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs282531	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs282542	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3172355	0.92[ASN][1000 genomes]
rs3732505	0.88[ASN][1000 genomes]
rs4681726	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4681736	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681738	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4681739	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4681903	0.88[ASN][1000 genomes]
rs4681904	0.83[ASN][1000 genomes]
rs4681937	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4681955	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4682001	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682002	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682008	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4974223	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4974225	0.82[EUR][1000 genomes]
rs55742226	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55810735	0.82[AMR][1000 genomes]
rs55828519	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56028632	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56172256	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56263252	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62251234	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6445811	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6445812	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6556	0.88[ASN][1000 genomes]
rs6764730	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6767903	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6794450	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72624856	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7612464	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7628343	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7633478	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7641898	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7645941	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7647095	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7648297	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7649872	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs873840	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9311609	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9311612	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs953540	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9809117	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9809741	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9814014	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9816100	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9816265	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9819952	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9826788	0.93[ASN][1000 genomes]
rs9830377	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9834239	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9835134	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9841851	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9847362	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9861577	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9864701	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9867302	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9868059	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9871265	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9872059	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9881152	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9883842	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7620896	CCDC66	cis	Whole Blood	GTEx
rs7620896	CCDC66	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 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	chr3:56718000-56723400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:56718000-56725200	Weak transcription	Dnd41	blood
8	chr3:56718000-56725200	Weak transcription	HMEC	breast
9	chr3:56718000-56727000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:56718000-56727400	Weak transcription	HSMMtube	muscle
11	chr3:56718200-56725000	Weak transcription	Placenta	Placenta
12	chr3:56718400-56723400	Weak transcription	HepG2	liver
13	chr3:56718400-56727000	Weak transcription	HSMM	muscle
14	chr3:56718800-56726600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:56719000-56725800	Weak transcription	Fetal Thymus	thymus
16	chr3:56721400-56724000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:56722200-56723600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:56722400-56726600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr3:56722400-56727000	Weak transcription	Primary B cells from cord blood	blood
20	chr3:56722600-56725200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:56722600-56726800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:56722800-56725200	Weak transcription	NHEK	skin
23	chr3:56723000-56723400	Weak transcription	GM12878-XiMat	blood

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