Variant report

Variant	rs12898455
Chromosome Location	chr15:34388914-34388915
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10152308	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152504	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851938	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12438470	0.85[ASN][1000 genomes]
rs12441615	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16958780	0.80[ASN][1000 genomes]
rs2339373	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34196590	0.84[ASN][1000 genomes]
rs3764237	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764238	0.84[ASN][1000 genomes]
rs60270549	0.81[ASN][1000 genomes]
rs62014675	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178266	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033335	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8037065	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972453	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456789	chr15:34034421-34426618	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv568920	chr15:34034421-34426618	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv471235	chr15:34035529-34421951	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1035579	chr15:34363159-34501115	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12898455	AVEN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34358600-34393000	Weak transcription	Aorta	Aorta
2	chr15:34368000-34391600	Weak transcription	Right Ventricle	heart
3	chr15:34368800-34392400	Weak transcription	Psoas Muscle	Psoas
4	chr15:34369600-34391600	Weak transcription	NHEK	skin
5	chr15:34372800-34393200	Weak transcription	Colonic Mucosa	Colon
6	chr15:34373600-34392400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr15:34374200-34392800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:34374400-34391600	Weak transcription	Fetal Brain Male	brain
9	chr15:34374800-34391600	Weak transcription	Small Intestine	intestine
10	chr15:34374800-34393000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr15:34375000-34392800	Weak transcription	Fetal Heart	heart
12	chr15:34375000-34393000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:34375600-34389000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr15:34375800-34391600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr15:34376000-34390200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:34376000-34392800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr15:34376800-34392400	Weak transcription	Brain Substantia Nigra	brain
18	chr15:34378400-34392400	Weak transcription	NHLF	lung
19	chr15:34378600-34392200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:34378600-34392600	Weak transcription	Fetal Kidney	kidney
21	chr15:34378800-34393000	Weak transcription	Lung	lung
22	chr15:34379000-34393000	Weak transcription	Esophagus	oesophagus
23	chr15:34380200-34391600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr15:34380200-34391800	Weak transcription	Brain Hippocampus Middle	brain
25	chr15:34380200-34392800	Weak transcription	HSMMtube	muscle
26	chr15:34380200-34393000	Weak transcription	Ovary	ovary
27	chr15:34380200-34393400	Weak transcription	Gastric	stomach
28	chr15:34380400-34391600	Weak transcription	Thymus	Thymus
29	chr15:34380400-34391800	Weak transcription	Left Ventricle	heart
30	chr15:34380400-34391800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr15:34380400-34391800	Weak transcription	Spleen	Spleen
32	chr15:34380400-34392400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr15:34380600-34391800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr15:34381000-34390200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr15:34381200-34391600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:34381200-34393400	Weak transcription	Pancreas	Pancrea
37	chr15:34382200-34392200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:34382400-34391600	Weak transcription	HepG2	liver
39	chr15:34382600-34391600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr15:34382600-34391600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr15:34382600-34392800	Weak transcription	Fetal Muscle Leg	muscle
42	chr15:34383400-34391600	Weak transcription	Brain Angular Gyrus	brain
43	chr15:34387000-34391600	Weak transcription	Fetal Stomach	stomach
44	chr15:34387000-34391800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr15:34387000-34392600	Weak transcription	Fetal Intestine Small	intestine
46	chr15:34387200-34390200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr15:34387400-34391400	Weak transcription	Primary T cells from cord blood	blood
48	chr15:34387400-34391600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:34387400-34391600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr15:34387400-34391600	Weak transcription	Fetal Intestine Large	intestine

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