Variant report

Variant	rs3794489
Chromosome Location	chr15:59525694-59525695
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10775169	0.89[EUR][1000 genomes]
rs11855088	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12437559	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12437571	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12439560	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12441621	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12593382	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12595677	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12912088	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12917076	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17236495	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17236502	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17302240	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17302247	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2306783	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2306784	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2414624	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28368974	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34310505	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34540528	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34827755	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4074433	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4074434	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4077169	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4287498	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4420472	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4482215	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4597251	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4775137	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56752228	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6494081	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6494091	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67037466	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67599725	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs68078916	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs68084852	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7166002	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7180541	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72625730	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72746841	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8030006	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1035868	chr15:59402426-59530594	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv833027	chr15:59474806-59608544	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv904272	chr15:59500577-59549018	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv904273	chr15:59518488-59567137	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59468200-59528600	Weak transcription	Stomach Mucosa	stomach
2	chr15:59502800-59525800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:59511400-59549200	Weak transcription	Colonic Mucosa	Colon
4	chr15:59515800-59566600	Weak transcription	Pancreas	Pancrea
5	chr15:59516600-59529400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:59517000-59530200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:59517000-59536600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:59517200-59528600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr15:59517200-59528800	Weak transcription	Primary B cells from cord blood	blood
10	chr15:59517200-59529000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:59517400-59529000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr15:59517400-59530000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr15:59517600-59528600	Weak transcription	HepG2	liver
14	chr15:59517600-59529000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr15:59517600-59546400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr15:59517800-59528600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr15:59517800-59564200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr15:59518000-59528800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr15:59520000-59528800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr15:59521600-59534400	Weak transcription	Placenta	Placenta
21	chr15:59521600-59566400	Weak transcription	Psoas Muscle	Psoas
22	chr15:59523000-59528200	Strong transcription	Liver	Liver
23	chr15:59523200-59527400	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr15:59524000-59541800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr15:59524000-59542200	Weak transcription	Gastric	stomach
26	chr15:59524000-59546200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:59524400-59526000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:59524400-59528800	Weak transcription	Fetal Intestine Large	intestine
29	chr15:59524600-59569200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr15:59524600-59574600	Weak transcription	Lung	lung
31	chr15:59524800-59529000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr15:59524800-59532800	Weak transcription	Fetal Intestine Small	intestine
33	chr15:59524800-59542200	Weak transcription	Esophagus	oesophagus
34	chr15:59525000-59526200	Weak transcription	GM12878-XiMat	blood
35	chr15:59525000-59531800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr15:59525000-59541800	Weak transcription	Fetal Muscle Leg	muscle
37	chr15:59525000-59546400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr15:59525200-59526000	Enhancers	HUVEC	blood vessel
39	chr15:59525200-59526400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr15:59525200-59526800	Weak transcription	Aorta	Aorta
41	chr15:59525200-59527400	Weak transcription	HMEC	breast
42	chr15:59525200-59527400	Weak transcription	HSMM	muscle
43	chr15:59525200-59528600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr15:59525200-59528600	Weak transcription	Brain Substantia Nigra	brain
45	chr15:59525200-59528800	Weak transcription	Adipose Nuclei	Adipose
46	chr15:59525200-59528800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr15:59525200-59529000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr15:59525200-59530000	Weak transcription	Left Ventricle	heart
49	chr15:59525200-59530200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr15:59525200-59530200	Weak transcription	NHLF	lung

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