Variant report

Variant	rs9841851
Chromosome Location	chr3:56639458-56639459
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10222629	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1054092	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1054093	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130525	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11130526	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11130527	0.84[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11712664	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11712799	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11719707	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11719726	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1316647	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13317989	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1388256	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1565378	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17216685	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17216747	0.81[ASN][1000 genomes]
rs17288852	0.86[ASN][1000 genomes]
rs1812347	0.86[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1873256	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2291498	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291500	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2317132	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs282525	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs282530	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs282531	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs282542	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3172355	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3732505	0.98[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4681726	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4681736	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4681738	0.81[ASN][1000 genomes]
rs4681903	0.98[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4681904	0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4681937	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4681955	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682001	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4682002	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4974221	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4974223	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4974225	0.94[EUR][1000 genomes]
rs55742226	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55828519	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55865922	0.80[ASN][1000 genomes]
rs56126040	0.80[ASN][1000 genomes]
rs56172256	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56263252	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56356916	0.86[ASN][1000 genomes]
rs62251234	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62255964	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6445811	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6445812	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6556	0.98[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6764730	0.90[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6767903	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6794450	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6799086	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7612464	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7620896	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7628343	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7633478	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7641898	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7645941	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7647095	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7648297	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7649872	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs873840	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9311609	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9311612	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs953540	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9809117	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9816100	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9816265	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9819952	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9826788	0.93[ASN][1000 genomes]
rs9830377	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9834239	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9835134	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9847362	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9861577	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9864701	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9867302	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9868059	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9871265	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9872059	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9881152	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9883842	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
rs9841851	CCDC66	Cis_1M	lymphoblastoid	RTeQTL
rs9841851	CCDC66	cis	Whole Blood	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
2	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
3	chr3:56592800-56644600	Weak transcription	Fetal Heart	heart
4	chr3:56600600-56640000	Weak transcription	NHLF	lung
5	chr3:56603200-56650400	Weak transcription	K562	blood
6	chr3:56603600-56640000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:56605600-56639600	Weak transcription	Pancreas	Pancrea
8	chr3:56605800-56639600	Weak transcription	Esophagus	oesophagus
9	chr3:56606200-56650200	Weak transcription	Colonic Mucosa	Colon
10	chr3:56607800-56639800	Weak transcription	HSMMtube	muscle
11	chr3:56607800-56650200	Weak transcription	Psoas Muscle	Psoas
12	chr3:56617200-56639600	Weak transcription	Aorta	Aorta
13	chr3:56617400-56639800	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:56617400-56639800	Weak transcription	Dnd41	blood
15	chr3:56619200-56639600	Weak transcription	Gastric	stomach
16	chr3:56619200-56639800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:56623000-56639600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:56624800-56639600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:56624800-56639800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:56625200-56639600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:56625200-56639600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:56625200-56639600	Weak transcription	HMEC	breast
23	chr3:56625200-56640000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:56625200-56640000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:56625200-56650400	Weak transcription	NHEK	skin
26	chr3:56625200-56653400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:56625600-56639600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:56626400-56656200	Weak transcription	Stomach Mucosa	stomach
29	chr3:56627600-56639600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:56627800-56639800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:56627800-56640000	Weak transcription	GM12878-XiMat	blood
32	chr3:56628200-56639600	Weak transcription	Brain Angular Gyrus	brain
33	chr3:56628200-56640000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr3:56628400-56639600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:56628400-56639800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr3:56628400-56640000	Weak transcription	Brain Anterior Caudate	brain
37	chr3:56628400-56640200	Weak transcription	Osteobl	bone
38	chr3:56628600-56640000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:56628600-56649600	Weak transcription	HepG2	liver
40	chr3:56629000-56647400	Weak transcription	HUVEC	blood vessel
41	chr3:56629000-56648000	Weak transcription	NH-A	brain
42	chr3:56629600-56640000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:56629600-56640000	Weak transcription	Primary B cells from peripheral blood	blood
44	chr3:56629600-56648200	Weak transcription	NHDF-Ad	bronchial
45	chr3:56629800-56639600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:56629800-56639800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr3:56630000-56639800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr3:56630000-56654400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr3:56630200-56639600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr3:56630200-56639600	Weak transcription	Duodenum Mucosa	Duodenum

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