Variant report

Variant	rs873840
Chromosome Location	chr3:56718804-56718805
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:56589231..56591997-chr3:56715959..56718849,3	K562	blood:
2	chr3:56702147..56705420-chr3:56716741..56719178,3	MCF-7	breast:
3	chr3:56589586..56592975-chr3:56714350..56719200,6	K562	blood:

Variant related genes	Relation type
ENSG00000180376	Chromatin interaction
ENSG00000163946	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10222629	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1054092	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1054093	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10865997	0.87[YRI][hapmap]
rs11130525	0.82[CEU][hapmap]
rs11130527	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11130542	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11712664	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11712799	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11719707	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11719726	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12486047	0.87[YRI][hapmap]
rs1316647	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13317989	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1388256	0.82[CEU][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1565378	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17216747	0.81[ASN][1000 genomes]
rs1812347	0.84[EUR][1000 genomes]
rs1873256	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291498	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291500	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2317132	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs282524	0.87[YRI][hapmap]
rs282525	1.00[CEU][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs282530	1.00[CEU][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs282531	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs282533	0.80[YRI][hapmap]
rs282542	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3172355	0.82[CEU][hapmap];0.93[ASN][1000 genomes]
rs3732505	0.82[CEU][hapmap];0.89[ASN][1000 genomes]
rs4681726	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4681736	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4681738	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4681739	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4681903	0.82[CEU][hapmap];0.89[ASN][1000 genomes]
rs4681904	0.85[ASN][1000 genomes]
rs4681937	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4681955	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4682001	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682002	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682008	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4974223	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55742226	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55810735	0.82[AMR][1000 genomes]
rs55828519	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56028632	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56172256	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56263252	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62251234	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6445811	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6445812	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6556	0.82[CEU][hapmap];0.89[ASN][1000 genomes]
rs6764730	0.84[EUR][1000 genomes]
rs6767903	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6769055	0.87[YRI][hapmap]
rs6794450	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72624856	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7612464	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7620896	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7628343	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7633478	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7641898	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7645941	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7647095	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7648297	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7649872	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9311609	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9311612	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs953540	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9809117	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9809741	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9814014	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9816100	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9816265	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9819952	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9826788	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9830377	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9834064	0.87[YRI][hapmap]
rs9834239	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9835134	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9841851	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9847362	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9861577	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9864701	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9867302	0.82[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9868059	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9871265	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9872059	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9881152	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9883842	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs873840	CCDC66	cis	Whole Blood	GTEx
rs873840	CCDC66	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 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	chr3:56717800-56719400	Weak transcription	Fetal Kidney	kidney
4	chr3:56717800-56720200	Weak transcription	Fetal Lung	lung
5	chr3:56717800-56720800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr3:56717800-56722000	Weak transcription	Primary B cells from cord blood	blood
7	chr3:56717800-56725200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:56717800-56725200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:56717800-56726800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:56718000-56719000	Strong transcription	Fetal Thymus	thymus
11	chr3:56718000-56719400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:56718000-56719600	Weak transcription	Fetal Stomach	stomach
13	chr3:56718000-56719800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:56718000-56722000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr3:56718000-56722200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr3:56718000-56723400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:56718000-56725200	Weak transcription	Dnd41	blood
18	chr3:56718000-56725200	Weak transcription	HMEC	breast
19	chr3:56718000-56727000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:56718000-56727400	Weak transcription	HSMMtube	muscle
21	chr3:56718200-56719000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
22	chr3:56718200-56722400	Weak transcription	NHEK	skin
23	chr3:56718200-56725000	Weak transcription	Placenta	Placenta
24	chr3:56718400-56719800	Weak transcription	NH-A	brain
25	chr3:56718400-56723400	Weak transcription	HepG2	liver
26	chr3:56718400-56727000	Weak transcription	HSMM	muscle
27	chr3:56718600-56721600	Weak transcription	GM12878-XiMat	blood
28	chr3:56718800-56719400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:56718800-56722200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:56718800-56726600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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