Variant report

Variant	rs4974221
Chromosome Location	chr3:56601939-56601940
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: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10222629	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11130525	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130526	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130527	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11719707	0.83[ASN][1000 genomes]
rs11719726	0.83[ASN][1000 genomes]
rs1316647	0.83[ASN][1000 genomes]
rs13317989	0.80[ASN][1000 genomes]
rs1388256	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17216685	0.82[AMR][1000 genomes]
rs1812347	0.83[EUR][1000 genomes]
rs2291498	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2291500	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2317132	0.87[ASN][1000 genomes]
rs282525	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs282530	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs282531	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs282542	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3172355	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3732505	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4681726	0.83[ASN][1000 genomes]
rs4681903	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4681904	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4681937	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4681955	0.83[ASN][1000 genomes]
rs4974223	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4974225	0.81[EUR][1000 genomes]
rs55742226	0.83[ASN][1000 genomes]
rs55865922	0.82[ASN][1000 genomes]
rs56126040	0.82[ASN][1000 genomes]
rs56263252	0.83[ASN][1000 genomes]
rs62255964	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6445811	0.83[ASN][1000 genomes]
rs6445812	0.83[ASN][1000 genomes]
rs6556	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6764730	0.83[EUR][1000 genomes]
rs6767903	0.81[ASN][1000 genomes]
rs6794450	0.81[ASN][1000 genomes]
rs6799086	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7612464	0.83[ASN][1000 genomes]
rs7628343	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7633478	0.81[ASN][1000 genomes]
rs7649872	0.83[ASN][1000 genomes]
rs9311609	0.83[ASN][1000 genomes]
rs953540	0.83[ASN][1000 genomes]
rs9809117	0.81[ASN][1000 genomes]
rs9816100	0.83[ASN][1000 genomes]
rs9816265	0.83[ASN][1000 genomes]
rs9819952	0.83[ASN][1000 genomes]
rs9826788	0.81[ASN][1000 genomes]
rs9830377	0.80[ASN][1000 genomes]
rs9834239	0.81[ASN][1000 genomes]
rs9841851	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9847362	0.81[ASN][1000 genomes]
rs9864701	0.83[ASN][1000 genomes]
rs9867302	0.83[ASN][1000 genomes]
rs9868059	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9871265	0.83[ASN][1000 genomes]
rs9881152	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9883842	0.83[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
rs4974221	CCDC66	Cis_1M	lymphoblastoid	RTeQTL
rs4974221	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	chr3:56592400-56602000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:56592400-56602800	Weak transcription	Esophagus	oesophagus
5	chr3:56592400-56602800	Weak transcription	Gastric	stomach
6	chr3:56592400-56602800	Weak transcription	Spleen	Spleen
7	chr3:56592400-56603000	Weak transcription	Pancreas	Pancrea
8	chr3:56592400-56607400	Weak transcription	Psoas Muscle	Psoas
9	chr3:56592400-56615600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
11	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
12	chr3:56592600-56602200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:56592600-56602200	Weak transcription	Brain Germinal Matrix	brain
14	chr3:56592600-56602200	Weak transcription	Fetal Brain Male	brain
15	chr3:56592600-56603000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:56592600-56603800	Weak transcription	Stomach Mucosa	stomach
17	chr3:56592800-56602000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:56592800-56602000	Weak transcription	Brain Angular Gyrus	brain
19	chr3:56592800-56602000	Weak transcription	A549	lung
20	chr3:56592800-56610200	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:56592800-56644600	Weak transcription	Fetal Heart	heart
22	chr3:56593000-56602200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:56593000-56603000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:56593000-56607800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:56593000-56610000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:56593200-56602000	Weak transcription	Brain Substantia Nigra	brain
27	chr3:56593200-56608000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:56593200-56609000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:56593200-56609600	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:56593200-56616400	Weak transcription	Colon Smooth Muscle	Colon
31	chr3:56593400-56602400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr3:56593400-56607600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:56593400-56608600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:56593600-56609800	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr3:56594000-56603000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr3:56594200-56602000	Strong transcription	HUVEC	blood vessel
37	chr3:56594200-56608000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:56594200-56610200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:56594400-56609400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:56594800-56604000	Strong transcription	Primary B cells from peripheral blood	blood
41	chr3:56594800-56609000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:56595400-56602000	Weak transcription	Brain Anterior Caudate	brain
43	chr3:56596000-56602200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:56596000-56605800	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr3:56596000-56608400	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr3:56596600-56602800	Weak transcription	NHDF-Ad	bronchial
47	chr3:56597200-56609200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:56597400-56609400	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:56597400-56610000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:56597600-56603800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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