Variant report

Variant	rs6478050
Chromosome Location	chr9:116755990-116755991
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:116753360..116755709-chr9:116755784..116758340,2	K562	blood:

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1006540	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1006541	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.92[ASN][1000 genomes]
rs10441747	1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs10513224	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs10739398	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs10759668	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.92[ASN][1000 genomes]
rs10759669	0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs10759670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10759671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10759672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10759673	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759674	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10759676	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs10817543	0.92[ASN][1000 genomes]
rs10817545	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10817546	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10817547	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]
rs10817548	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817555	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs10817556	0.86[ASN][1000 genomes]
rs10982029	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs10982031	0.91[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10982032	0.86[ASN][1000 genomes]
rs11788583	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs11788633	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs11788661	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs11791155	0.95[CHB][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.84[ASN][1000 genomes]
rs11791230	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12551686	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs12682865	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs12686727	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs13285834	0.94[ASN][1000 genomes]
rs13298270	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs1330171	0.95[CHB][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1408112	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1408113	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1408114	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1535762	0.91[CHB][hapmap]
rs1535763	0.91[CHB][hapmap]
rs1535764	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs1886129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1928699	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2026139	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2116407	0.81[CHB][hapmap]
rs2418262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2418263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3748183	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs4497041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4641141	0.84[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.95[ASN][1000 genomes]
rs4978561	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs4978562	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4979310	0.95[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs4979311	0.95[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs4979316	0.95[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs4979317	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs4979318	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs4979319	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs4979320	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4979321	0.86[CHB][hapmap]
rs4979322	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs4979323	0.90[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs4979324	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs4979326	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs4979327	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs56221603	0.86[ASN][1000 genomes]
rs7020561	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7023499	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7026668	0.91[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs7031814	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7032124	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7032729	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs7034528	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7036001	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7036201	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036206	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7041487	0.91[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs7041524	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs7042021	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7042081	0.81[ASN][1000 genomes]
rs7850217	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7858120	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs7863348	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7863469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814701	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs860082	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.92[ASN][1000 genomes]
rs9332459	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs942286	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs942287	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs9695257	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs9696305	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[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
rs6478050	DEC1	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116721200-116756400	Weak transcription	NHEK	skin
2	chr9:116732200-116768800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr9:116732200-116773400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:116732600-116762600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr9:116733000-116768600	Weak transcription	Fetal Kidney	kidney
6	chr9:116733400-116800200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:116736400-116783000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr9:116741400-116756200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr9:116746400-116756600	Strong transcription	Fetal Intestine Small	intestine
10	chr9:116747600-116756200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:116749000-116756800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:116749400-116756400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr9:116749800-116759200	Enhancers	Liver	Liver
14	chr9:116750000-116756800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:116750200-116756200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr9:116750200-116756800	Enhancers	HSMMtube	muscle
17	chr9:116751000-116773400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr9:116752000-116764600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr9:116752200-116756000	Weak transcription	Small Intestine	intestine
20	chr9:116752200-116760000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr9:116752200-116764200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:116752400-116756000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr9:116752400-116757000	Enhancers	Lung	lung
24	chr9:116752400-116762000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr9:116752600-116756200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr9:116752800-116757200	Enhancers	Stomach Mucosa	stomach
27	chr9:116752800-116762600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr9:116753000-116756400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:116753000-116756400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr9:116753000-116756600	Enhancers	Spleen	Spleen
31	chr9:116753200-116756000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr9:116753200-116756400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:116753400-116757000	Enhancers	Left Ventricle	heart
34	chr9:116753400-116757000	Enhancers	Right Atrium	heart
35	chr9:116753400-116758400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:116753400-116758800	Weak transcription	Fetal Intestine Large	intestine
37	chr9:116753600-116756200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr9:116753600-116756800	Enhancers	Ovary	ovary
39	chr9:116753600-116757000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr9:116753600-116757000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr9:116753600-116757200	Enhancers	Fetal Muscle Leg	muscle
42	chr9:116753600-116764000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr9:116753600-116764000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr9:116753600-116764600	Weak transcription	A549	lung
45	chr9:116753800-116756000	Weak transcription	NHLF	lung
46	chr9:116753800-116756200	Weak transcription	HMEC	breast
47	chr9:116753800-116756800	Enhancers	Fetal Muscle Trunk	muscle
48	chr9:116753800-116757000	Enhancers	Pancreas	Pancrea
49	chr9:116754000-116756800	Enhancers	Duodenum Mucosa	Duodenum
50	chr9:116754000-116756800	Enhancers	Fetal Thymus	thymus

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