Variant report

Variant	rs12912088
Chromosome Location	chr15:59529301-59529302
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10775169	0.93[EUR][1000 genomes]
rs11855088	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12437559	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12437571	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12439560	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12441621	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12443328	0.90[CEU][hapmap]
rs12593382	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12595677	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12917076	0.90[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17236495	0.80[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17236502	0.82[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17236509	0.80[CEU][hapmap]
rs17302240	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17302247	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2306783	0.90[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2306784	0.90[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2414624	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28368974	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34310505	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34540528	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34827755	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3794489	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4074433	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4074434	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4077169	0.80[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4287498	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4420472	0.82[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4482215	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4597251	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4775137	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56752228	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6494081	0.80[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6494091	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67037466	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67599725	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs68078916	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs68084852	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7166002	0.81[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7180541	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72625730	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72746841	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8030006	0.83[AMR][1000 genomes];0.82[EUR][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:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59511400-59549200	Weak transcription	Colonic Mucosa	Colon
2	chr15:59515800-59566600	Weak transcription	Pancreas	Pancrea
3	chr15:59516600-59529400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:59517000-59530200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:59517000-59536600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:59517400-59530000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr15:59517600-59546400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr15:59517800-59564200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr15:59521600-59534400	Weak transcription	Placenta	Placenta
10	chr15:59521600-59566400	Weak transcription	Psoas Muscle	Psoas
11	chr15:59524000-59541800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:59524000-59542200	Weak transcription	Gastric	stomach
13	chr15:59524000-59546200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:59524600-59569200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:59524600-59574600	Weak transcription	Lung	lung
16	chr15:59524800-59532800	Weak transcription	Fetal Intestine Small	intestine
17	chr15:59524800-59542200	Weak transcription	Esophagus	oesophagus
18	chr15:59525000-59531800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr15:59525000-59541800	Weak transcription	Fetal Muscle Leg	muscle
20	chr15:59525000-59546400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr15:59525200-59530000	Weak transcription	Left Ventricle	heart
22	chr15:59525200-59530200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr15:59525200-59530200	Weak transcription	NHLF	lung
24	chr15:59525200-59532000	Weak transcription	Brain Hippocampus Middle	brain
25	chr15:59525200-59532400	Weak transcription	Ovary	ovary
26	chr15:59525200-59532800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr15:59525200-59533000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr15:59525200-59533000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr15:59525200-59533200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr15:59525200-59540200	Weak transcription	Right Ventricle	heart
31	chr15:59525200-59543000	Weak transcription	Right Atrium	heart
32	chr15:59525200-59547800	Weak transcription	Colon Smooth Muscle	Colon
33	chr15:59525200-59554000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr15:59525200-59566600	Weak transcription	Small Intestine	intestine
35	chr15:59525200-59582000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr15:59525400-59529400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr15:59525400-59534800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:59525400-59541000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:59525400-59542200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr15:59525600-59529800	Weak transcription	NHDF-Ad	bronchial
41	chr15:59525600-59530000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr15:59525600-59530000	Weak transcription	Osteobl	bone
43	chr15:59525600-59530200	Strong transcription	Hela-S3	cervix
44	chr15:59526600-59530000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr15:59526800-59530000	Weak transcription	NHEK	skin
46	chr15:59527400-59529400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr15:59527400-59534600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr15:59527400-59536000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:59527600-59532800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr15:59528000-59533000	Weak transcription	HSMM	muscle

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