Variant report

Variant	rs4974223
Chromosome Location	chr3:56602088-56602089
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	chr3:56590931..56593644-chr3:56601004..56602846,2	K562	blood:

Variant related genes	Relation type
ENSG00000180376	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10222629	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1054092	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1054093	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10865997	0.81[AMR][1000 genomes]
rs11130525	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130526	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130527	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs11712664	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11712799	0.85[EUR][1000 genomes]
rs11719707	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11719726	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12486047	0.81[AMR][1000 genomes]
rs1316647	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13317989	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1388256	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1565378	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17216685	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17288852	0.81[ASN][1000 genomes]
rs1812347	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1873256	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2291498	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2291500	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2317132	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs282525	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs282530	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs282531	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs282542	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3172355	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3732505	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4681726	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4681736	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4681903	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4681904	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4681937	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4681955	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4682001	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4682002	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4974218	0.81[AMR][1000 genomes]
rs4974221	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4974222	0.81[AMR][1000 genomes]
rs4974225	0.90[EUR][1000 genomes]
rs55742226	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55828519	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55865922	0.87[ASN][1000 genomes]
rs55960262	0.85[ASN][1000 genomes]
rs56126040	0.87[ASN][1000 genomes]
rs56263252	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56356916	0.81[ASN][1000 genomes]
rs62251234	0.84[ASN][1000 genomes]
rs62255964	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6445811	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6445812	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6556	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6764730	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6767903	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6769055	0.81[AMR][1000 genomes]
rs6794450	0.87[ASN][1000 genomes]
rs6799086	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7612464	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7620896	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7628343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633478	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7641898	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7645941	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7647095	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7648297	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7649872	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs873840	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9311609	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9311612	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs953540	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9809117	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9816100	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9816265	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9819952	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9826788	0.87[ASN][1000 genomes]
rs9830377	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9834239	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9835134	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9841851	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9847362	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9861577	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9864701	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9867302	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9868059	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9871265	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9872059	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9881152	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883842	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347557	chr3:56466500-56619322	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv460557	chr3:56594735-56661320	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv590362	chr3:56594735-56661320	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4974223	CCDC66	Cis_1M	lymphoblastoid	RTeQTL
rs4974223	CCDC66	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56592000-56615600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:56592200-56609400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:56592400-56602800	Weak transcription	Esophagus	oesophagus
4	chr3:56592400-56602800	Weak transcription	Gastric	stomach
5	chr3:56592400-56602800	Weak transcription	Spleen	Spleen
6	chr3:56592400-56603000	Weak transcription	Pancreas	Pancrea
7	chr3:56592400-56607400	Weak transcription	Psoas Muscle	Psoas
8	chr3:56592400-56615600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
10	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
11	chr3:56592600-56602200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:56592600-56602200	Weak transcription	Brain Germinal Matrix	brain
13	chr3:56592600-56602200	Weak transcription	Fetal Brain Male	brain
14	chr3:56592600-56603000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:56592600-56603800	Weak transcription	Stomach Mucosa	stomach
16	chr3:56592800-56610200	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:56592800-56644600	Weak transcription	Fetal Heart	heart
18	chr3:56593000-56602200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:56593000-56603000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:56593000-56607800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:56593000-56610000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:56593200-56608000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:56593200-56609000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:56593200-56609600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:56593200-56616400	Weak transcription	Colon Smooth Muscle	Colon
26	chr3:56593400-56602400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:56593400-56607600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:56593400-56608600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:56593600-56609800	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr3:56594000-56603000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr3:56594200-56608000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:56594200-56610200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:56594400-56609400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:56594800-56604000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr3:56594800-56609000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:56596000-56602200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:56596000-56605800	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr3:56596000-56608400	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:56596600-56602800	Weak transcription	NHDF-Ad	bronchial
40	chr3:56597200-56609200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:56597400-56609400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr3:56597400-56610000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:56597600-56603800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr3:56597600-56605400	Strong transcription	Hela-S3	cervix
45	chr3:56597600-56608000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:56597800-56603800	Strong transcription	NH-A	brain
47	chr3:56597800-56607600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr3:56598000-56607000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:56598000-56607800	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr3:56598000-56609200	Strong transcription	Fetal Thymus	thymus

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