Variant report

Variant	rs10817547
Chromosome Location	chr9:116751850-116751851
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1006540	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs1006541	0.95[CHB][hapmap];0.80[GIH][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap]
rs10441747	0.95[CHB][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10513224	0.95[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs10739398	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10759668	0.95[CHB][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap];0.80[ASN][1000 genomes]
rs10759669	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10759670	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10759671	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10759672	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10759673	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10759674	0.90[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10759675	0.88[ASN][1000 genomes]
rs10759676	0.91[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs10817543	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10817544	0.93[ASN][1000 genomes]
rs10817545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10817546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10817548	1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10817549	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10817552	0.82[ASN][1000 genomes]
rs10817555	0.91[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs10982026	0.87[ASN][1000 genomes]
rs10982029	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10982031	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs10982034	0.83[ASN][1000 genomes]
rs11788583	0.95[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11788633	0.91[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11788661	0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11788667	0.83[ASN][1000 genomes]
rs11791155	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.99[ASN][1000 genomes]
rs11791230	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs12551686	0.91[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs12682865	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs12686727	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13285834	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13298270	0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1330171	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1408112	0.95[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs1408113	0.95[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs1408114	0.95[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1535762	0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs1535763	0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs1535764	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs1886129	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1928699	0.91[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs2026139	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2418262	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2418263	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3748182	0.84[ASN][1000 genomes]
rs3748183	0.91[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs3860174	0.81[CHB][hapmap]
rs4497041	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4641141	0.84[ASW][hapmap];0.91[CHB][hapmap];0.80[GIH][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4978561	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4978562	0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4979310	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs4979311	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs4979316	0.91[CHB][hapmap]
rs4979317	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4979318	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4979319	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4979320	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4979321	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs4979322	0.91[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4979323	0.85[CHB][hapmap]
rs4979324	0.86[CHB][hapmap]
rs4979326	0.91[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4979327	0.91[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs6478050	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7020561	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs7023499	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7026668	0.86[CHB][hapmap]
rs7031814	0.94[CHB][hapmap];0.93[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7032124	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7032729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap]
rs7034528	0.95[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs7036001	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7036201	0.94[CHB][hapmap];0.86[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7036206	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7041487	0.86[CHB][hapmap]
rs7041524	0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7042021	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs7850217	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7858120	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7863348	0.94[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7863469	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs814701	0.95[CHB][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap];0.81[ASN][1000 genomes]
rs860082	0.95[CHB][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap];0.80[ASN][1000 genomes]
rs9332459	0.95[CHB][hapmap];0.83[JPT][hapmap];0.80[AMR][1000 genomes]
rs942286	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs942287	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9695257	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs9696305	0.95[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]

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
rs10817547	DEC1	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116717200-116754600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr9:116720400-116754200	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr9:116721200-116756400	Weak transcription	NHEK	skin
4	chr9:116728200-116754600	Weak transcription	Thymus	Thymus
5	chr9:116731800-116755600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr9:116732000-116753000	Weak transcription	Esophagus	oesophagus
7	chr9:116732200-116753800	Weak transcription	Fetal Brain Female	brain
8	chr9:116732200-116754200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr9:116732200-116768800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr9:116732200-116773400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr9:116732600-116762600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr9:116733000-116768600	Weak transcription	Fetal Kidney	kidney
13	chr9:116733400-116800200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:116735800-116754200	Weak transcription	Right Ventricle	heart
15	chr9:116736400-116783000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr9:116736600-116754000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr9:116738800-116753400	Weak transcription	Brain Anterior Caudate	brain
18	chr9:116738800-116753800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr9:116740200-116752800	Weak transcription	Stomach Mucosa	stomach
20	chr9:116741200-116754400	Weak transcription	Colon Smooth Muscle	Colon
21	chr9:116741400-116756200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr9:116741600-116754800	Weak transcription	Primary B cells from cord blood	blood
23	chr9:116744000-116753200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:116746400-116756600	Strong transcription	Fetal Intestine Small	intestine
25	chr9:116746800-116753800	Genic enhancers	Fetal Muscle Trunk	muscle
26	chr9:116747000-116752000	Weak transcription	Colonic Mucosa	Colon
27	chr9:116747000-116752400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr9:116747600-116756200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr9:116748000-116752600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr9:116748200-116754200	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr9:116748400-116752600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr9:116748600-116754200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr9:116748800-116755800	Weak transcription	NH-A	brain
34	chr9:116749000-116753200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr9:116749000-116756800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr9:116749200-116753200	Weak transcription	Brain Angular Gyrus	brain
37	chr9:116749200-116755600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr9:116749400-116756400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr9:116749800-116753000	Strong transcription	HUVEC	blood vessel
40	chr9:116749800-116754800	Enhancers	Placenta	Placenta
41	chr9:116749800-116759200	Enhancers	Liver	Liver
42	chr9:116750000-116752200	Strong transcription	NHLF	lung
43	chr9:116750000-116752400	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr9:116750000-116754400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:116750000-116756800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr9:116750200-116752600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr9:116750200-116753400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr9:116750200-116753400	Strong transcription	Fetal Intestine Large	intestine
49	chr9:116750200-116753600	Strong transcription	A549	lung
50	chr9:116750200-116755600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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