Variant report

Variant	rs11130542
Chromosome Location	chr3:56730584-56730585
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:56716242..56719053-chr3:56730273..56732259,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163946	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1054092	0.86[EUR][1000 genomes]
rs1054093	0.86[EUR][1000 genomes]
rs11719726	0.80[EUR][1000 genomes]
rs1316647	0.83[EUR][1000 genomes]
rs13317989	0.86[EUR][1000 genomes]
rs1565378	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1873256	0.86[EUR][1000 genomes]
rs4681726	0.83[EUR][1000 genomes]
rs4681736	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4681738	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4681739	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4681955	0.83[EUR][1000 genomes]
rs4682001	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4682002	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4682008	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55742226	0.80[EUR][1000 genomes]
rs55828519	0.86[EUR][1000 genomes]
rs56028632	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56172256	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62251234	0.82[EUR][1000 genomes]
rs6445811	0.83[EUR][1000 genomes]
rs6445812	0.83[EUR][1000 genomes]
rs6767903	0.86[EUR][1000 genomes]
rs6794450	0.82[EUR][1000 genomes]
rs72624856	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7612464	0.83[EUR][1000 genomes]
rs7620896	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7633478	0.86[EUR][1000 genomes]
rs7641898	0.86[EUR][1000 genomes]
rs7645941	0.86[EUR][1000 genomes]
rs7647095	0.86[EUR][1000 genomes]
rs7648297	0.86[EUR][1000 genomes]
rs7649872	0.81[EUR][1000 genomes]
rs873840	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9311609	0.83[EUR][1000 genomes]
rs9311612	0.86[EUR][1000 genomes]
rs953540	0.83[EUR][1000 genomes]
rs9809117	0.86[EUR][1000 genomes]
rs9809741	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9814014	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816100	0.83[EUR][1000 genomes]
rs9816265	0.83[EUR][1000 genomes]
rs9819952	0.81[EUR][1000 genomes]
rs9830377	0.86[EUR][1000 genomes]
rs9834239	0.83[EUR][1000 genomes]
rs9835134	0.86[EUR][1000 genomes]
rs9847362	0.83[EUR][1000 genomes]
rs9861577	0.86[EUR][1000 genomes]
rs9864701	0.83[EUR][1000 genomes]
rs9867302	0.83[EUR][1000 genomes]
rs9871265	0.83[EUR][1000 genomes]
rs9872059	0.86[EUR][1000 genomes]
rs9883842	0.83[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11130542	CCDC66	cis	Whole Blood	GTEx
rs11130542	CCDC66	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56725800-56734000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:56726000-56734000	Weak transcription	NHEK	skin
3	chr3:56727600-56731000	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr3:56727600-56731200	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr3:56727600-56731200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr3:56727800-56731000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:56727800-56731200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr3:56728000-56733000	Weak transcription	Placenta	Placenta
9	chr3:56728200-56731000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr3:56729200-56731000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr3:56729200-56731200	Enhancers	Primary T cells from cord blood	blood
12	chr3:56729200-56731200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:56729600-56730600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr3:56729600-56730600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:56729600-56730600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:56729600-56730800	Weak transcription	Primary B cells from cord blood	blood
17	chr3:56729600-56730800	Weak transcription	Primary B cells from peripheral blood	blood
18	chr3:56729600-56730800	Weak transcription	GM12878-XiMat	blood
19	chr3:56729800-56731000	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr3:56729800-56738600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr3:56730000-56733000	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr3:56730000-56738600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr3:56730400-56731200	Enhancers	Primary T cells fromperipheralblood	blood
24	chr3:56730400-56731200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:56730400-56738600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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