Variant report

Variant	rs7041524
Chromosome Location	chr9:116774399-116774400
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116768367..116772045-chr9:116772665..116776100,5	MCF-7	breast:
2	chr9:116773678..116775995-chr9:116779298..116781749,2	K562	blood:
3	chr9:116773482..116775850-chr9:116777082..116779157,3	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:105)

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];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10759668	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs10759669	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[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	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10759676	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10817545	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10817546	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10817547	0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10817548	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs10817552	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10817553	0.94[ASN][1000 genomes]
rs10817555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10817556	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10817558	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10982026	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10982029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10982031	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10982032	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10982034	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10982042	0.88[CEU][hapmap];0.81[CHB][hapmap];0.91[EUR][1000 genomes]
rs11788583	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs11788633	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11788661	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11788667	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11790678	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11791155	0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11791230	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12551686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12682865	0.91[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs12686226	0.88[CEU][hapmap];0.85[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12686727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13298270	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1330171	0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[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];0.86[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];0.83[AMR][1000 genomes];0.92[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];0.86[CHD][hapmap]
rs2078305	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes];0.92[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	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3748182	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3748183	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3860174	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[EUR][1000 genomes]
rs4497041	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs4641141	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs4978561	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4978562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4979310	0.91[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs4979311	0.91[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs4979316	0.91[CHB][hapmap]
rs4979317	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4979318	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4979319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4979320	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]
rs4979321	1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs4979322	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4979323	0.95[CHB][hapmap]
rs4979324	0.95[CHB][hapmap]
rs4979326	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4979327	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.98[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[GIH][hapmap];0.89[JPT][hapmap]
rs7023499	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs7026668	0.95[CHB][hapmap]
rs7028504	0.94[ASN][1000 genomes]
rs7030167	1.00[CEU][hapmap];0.87[TSI][hapmap];0.96[EUR][1000 genomes]
rs7031814	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs7032729	0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7034528	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs7035891	0.91[EUR][1000 genomes]
rs7036001	0.85[ASN][1000 genomes]
rs7036201	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7036206	0.85[ASN][1000 genomes]
rs7041360	1.00[CEU][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes]
rs7041487	0.95[CHB][hapmap]
rs7042021	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7850217	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs7858120	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs942287	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9695257	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs9696305	0.86[CHB][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv521361	chr9:116774010-116780992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7041524	DEC1	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116733400-116800200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:116736400-116783000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:116756400-116775600	Weak transcription	Primary B cells from cord blood	blood
4	chr9:116756800-116779000	Weak transcription	Esophagus	oesophagus
5	chr9:116756800-116783800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr9:116757000-116779600	Weak transcription	Colon Smooth Muscle	Colon
7	chr9:116757000-116779800	Weak transcription	Colonic Mucosa	Colon
8	chr9:116757000-116783400	Weak transcription	Small Intestine	intestine
9	chr9:116758400-116775000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:116762200-116775400	Strong transcription	Liver	Liver
11	chr9:116762200-116780400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr9:116762400-116776800	Strong transcription	Fetal Intestine Large	intestine
13	chr9:116763800-116777000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:116764600-116797200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr9:116765000-116783200	Weak transcription	NHEK	skin
16	chr9:116765800-116784400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr9:116766000-116784800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr9:116766000-116792600	Weak transcription	Stomach Mucosa	stomach
19	chr9:116766000-116798000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr9:116766200-116775000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:116766200-116799000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr9:116766400-116774400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:116766600-116782400	Strong transcription	A549	lung
24	chr9:116766600-116811200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr9:116766800-116775000	Strong transcription	Fetal Lung	lung
26	chr9:116767000-116774400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr9:116767000-116780400	Weak transcription	Brain Angular Gyrus	brain
28	chr9:116767200-116779000	Weak transcription	Brain Hippocampus Middle	brain
29	chr9:116767200-116779400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr9:116767200-116785800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr9:116767400-116776200	Weak transcription	Brain Anterior Caudate	brain
32	chr9:116768000-116775000	Strong transcription	Fetal Muscle Trunk	muscle
33	chr9:116768000-116777000	Strong transcription	HSMM	muscle
34	chr9:116768400-116794600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr9:116768800-116778800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr9:116768800-116784800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr9:116769000-116775200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr9:116769200-116774800	Strong transcription	Fetal Stomach	stomach
39	chr9:116769200-116779000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr9:116769400-116775400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr9:116769400-116778000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr9:116769400-116780200	Weak transcription	Thymus	Thymus
43	chr9:116769400-116790400	Weak transcription	Right Ventricle	heart
44	chr9:116770400-116779800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr9:116771000-116774400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr9:116771000-116779000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr9:116771200-116774400	Weak transcription	Fetal Brain Female	brain
48	chr9:116771200-116779200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr9:116771400-116779200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr9:116771600-116778400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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