Variant report

Variant	rs56172256
Chromosome Location	chr3:56727780-56727781
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:56708568..56710932-chr3:56727678..56729297,2	MCF-7	breast:
2	chr3:56715572..56717883-chr3:56727378..56729582,3	MCF-7	breast:
3	chr3:56726200..56728005-chr3:56842796..56845095,2	MCF-7	breast:
4	chr3:56716408..56719347-chr3:56726422..56729753,3	K562	blood:

Variant related genes	Relation type
ENSG00000163946	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10222629	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1054092	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1054093	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130527	0.82[EUR][1000 genomes]
rs11130542	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11712664	0.80[ASN][1000 genomes]
rs11719707	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11719726	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1316647	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13317989	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1388256	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1565378	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1812347	0.82[EUR][1000 genomes]
rs1873256	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291498	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2291500	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2317132	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs282525	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs282530	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs282531	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs282542	0.80[EUR][1000 genomes]
rs3172355	0.86[ASN][1000 genomes]
rs3732505	0.82[ASN][1000 genomes]
rs4681726	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4681736	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4681738	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681739	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4681903	0.82[ASN][1000 genomes]
rs4681937	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4681955	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4682001	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682002	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682008	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55742226	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55828519	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56028632	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56263252	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62251234	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6445811	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6445812	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6556	0.82[ASN][1000 genomes]
rs6764730	0.82[EUR][1000 genomes]
rs6767903	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6794450	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72624856	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7612464	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7620896	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7633478	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7641898	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7645941	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7647095	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7648297	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7649872	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs873840	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9311609	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9311612	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs953540	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9809117	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9809741	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9814014	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9816100	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9816265	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9819952	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9826788	0.88[ASN][1000 genomes]
rs9830377	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9834239	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9835134	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9841851	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9847362	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9861577	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9864701	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9867302	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9868059	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9871265	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9872059	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9883842	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56172256	CCDC66	cis	Whole Blood	GTEx
rs56172256	CCDC66	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 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	chr3:56726000-56727800	Weak transcription	Placenta	Placenta
3	chr3:56726000-56734000	Weak transcription	NHEK	skin
4	chr3:56726200-56729200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:56726400-56729800	Enhancers	Fetal Thymus	thymus
6	chr3:56726600-56729600	Enhancers	Primary B cells from peripheral blood	blood
7	chr3:56726600-56730000	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr3:56726800-56728000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr3:56726800-56728000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:56726800-56728000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:56726800-56728200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr3:56726800-56728200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:56726800-56729600	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr3:56726800-56729600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:56727000-56727800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:56727000-56727800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr3:56727000-56728000	Enhancers	Rectal Mucosa Donor 29	rectum
18	chr3:56727000-56728000	Enhancers	HSMM	muscle
19	chr3:56727000-56728200	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr3:56727000-56728200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr3:56727000-56729600	Enhancers	Primary hematopoietic stem cells	blood
22	chr3:56727200-56728000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:56727200-56729600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:56727200-56729800	Enhancers	Thymus	Thymus
25	chr3:56727200-56730000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:56727400-56727800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr3:56727400-56728000	Enhancers	HSMMtube	muscle
28	chr3:56727400-56728200	Enhancers	Duodenum Mucosa	Duodenum
29	chr3:56727400-56728400	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr3:56727600-56728000	Enhancers	Dnd41	blood
31	chr3:56727600-56728200	Enhancers	HUVEC	blood vessel
32	chr3:56727600-56729600	Enhancers	Primary B cells from cord blood	blood
33	chr3:56727600-56729600	Enhancers	GM12878-XiMat	blood
34	chr3:56727600-56729800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr3:56727600-56730000	Enhancers	Primary T cells fromperipheralblood	blood
36	chr3:56727600-56730400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:56727600-56731000	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr3:56727600-56731200	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr3:56727600-56731200	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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