Variant report

Variant	rs4979320
Chromosome Location	chr9:116766277-116766278
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1006540	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs1006541	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs1008138	0.82[CHB][hapmap]
rs10441747	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs10513224	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs10739398	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10759668	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs10759669	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10759670	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs10759671	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs10759672	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs10759674	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs10759675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10759676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10817544	0.82[ASN][1000 genomes]
rs10817545	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10817546	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10817547	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10817548	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs10817552	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10817553	0.91[ASN][1000 genomes]
rs10817555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10817556	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10817558	0.89[EUR][1000 genomes]
rs10982026	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10982029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10982031	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10982032	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10982034	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10982042	0.88[CEU][hapmap];0.81[CHB][hapmap];0.88[EUR][1000 genomes]
rs11788583	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs11788633	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11788661	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11788667	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11790678	0.88[EUR][1000 genomes]
rs11791155	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11791230	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12551686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12682865	0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs12686226	0.88[CEU][hapmap];0.85[CHB][hapmap];0.89[EUR][1000 genomes]
rs12686727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13298270	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1330171	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1408112	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs1408113	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs1408114	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs1408115	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs1535762	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs1535763	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs1535764	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs1590367	0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[EUR][1000 genomes]
rs1886129	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs1928699	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs1965753	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs2078305	0.88[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.89[EUR][1000 genomes]
rs2116407	0.86[CHB][hapmap]
rs2418262	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2418263	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs35841848	0.89[EUR][1000 genomes]
rs3748182	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3748183	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3860174	0.88[CEU][hapmap];0.91[CHB][hapmap];0.87[EUR][1000 genomes]
rs4497041	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs4641141	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs4978561	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4978562	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4979310	0.91[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4979311	0.91[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4979316	0.91[CHB][hapmap]
rs4979317	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4979318	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4979319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979321	1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs4979322	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4979323	0.95[CHB][hapmap]
rs4979324	0.95[CHB][hapmap]
rs4979326	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4979327	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4979331	0.86[CHB][hapmap]
rs6478050	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs7020561	0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap]
rs7023499	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs7026668	0.95[CHB][hapmap]
rs7028504	0.92[ASN][1000 genomes]
rs7030167	1.00[CEU][hapmap];0.82[TSI][hapmap];0.93[EUR][1000 genomes]
rs7031814	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs7032729	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7034528	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs7035891	0.88[EUR][1000 genomes]
rs7036001	0.88[ASN][1000 genomes]
rs7036201	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7036206	0.88[ASN][1000 genomes]
rs7041360	1.00[CEU][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs7041487	0.95[CHB][hapmap]
rs7041524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7042021	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7850217	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs7858120	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7863348	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs814701	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs860082	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs9332459	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs942286	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs942287	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9695257	0.91[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs9696305	0.86[CHB][hapmap];0.83[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4979320	DEC1	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116732200-116768800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr9:116732200-116773400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr9:116733000-116768600	Weak transcription	Fetal Kidney	kidney
4	chr9:116733400-116800200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:116736400-116783000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:116751000-116773400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr9:116755400-116768000	Weak transcription	HSMM	muscle
8	chr9:116756200-116773800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr9:116756400-116775600	Weak transcription	Primary B cells from cord blood	blood
10	chr9:116756600-116766400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr9:116756800-116768000	Weak transcription	Thymus	Thymus
12	chr9:116756800-116768800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr9:116756800-116779000	Weak transcription	Esophagus	oesophagus
14	chr9:116756800-116783800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr9:116757000-116770200	Weak transcription	Aorta	Aorta
16	chr9:116757000-116773600	Weak transcription	HMEC	breast
17	chr9:116757000-116779600	Weak transcription	Colon Smooth Muscle	Colon
18	chr9:116757000-116779800	Weak transcription	Colonic Mucosa	Colon
19	chr9:116757000-116783400	Weak transcription	Small Intestine	intestine
20	chr9:116757600-116772200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr9:116758200-116767400	Strong transcription	Fetal Intestine Small	intestine
22	chr9:116758400-116775000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:116760000-116773400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:116760800-116771600	Strong transcription	NHLF	lung
25	chr9:116762200-116766400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:116762200-116766600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr9:116762200-116770800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr9:116762200-116772800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr9:116762200-116775400	Strong transcription	Liver	Liver
30	chr9:116762200-116780400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr9:116762400-116776800	Strong transcription	Fetal Intestine Large	intestine
32	chr9:116762600-116766600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr9:116762800-116768000	Enhancers	Placenta	Placenta
34	chr9:116763000-116769400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:116763400-116768000	Genic enhancers	Fetal Muscle Trunk	muscle
36	chr9:116763800-116777000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr9:116764000-116766600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr9:116764000-116768000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr9:116764000-116772200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr9:116764200-116766400	Enhancers	Brain Hippocampus Middle	brain
41	chr9:116764200-116767200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr9:116764200-116767400	Enhancers	Fetal Heart	heart
43	chr9:116764400-116767400	Enhancers	Fetal Brain Male	brain
44	chr9:116764400-116767600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr9:116764400-116768000	Genic enhancers	Fetal Muscle Leg	muscle
46	chr9:116764400-116771000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr9:116764600-116767000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr9:116764600-116767400	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr9:116764600-116767800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr9:116764600-116797200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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