Variant report

Variant	rs12461416
Chromosome Location	chr19:45609166-45609167
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:45602690..45605477-chr19:45607182..45610015,3	K562	blood:
2	chr19:45606192..45609291-chr19:45618096..45620954,3	K562	blood:

Variant related genes	Relation type
ENSG00000104866	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10403214	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10405306	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10405719	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10405721	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10407374	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10408366	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10409138	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs10409232	0.91[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10409727	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10409903	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10410424	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10412988	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10417101	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10417618	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10417804	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10421932	0.92[CEU][hapmap];0.88[YRI][hapmap]
rs10424651	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12459945	0.80[EUR][1000 genomes]
rs1541926	1.00[EUR][1000 genomes]
rs17562676	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17562787	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17642665	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1982077	1.00[EUR][1000 genomes]
rs2011438	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4608431	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4803798	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7257566	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7257599	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs733289	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73562250	0.80[EUR][1000 genomes]
rs73562267	0.80[EUR][1000 genomes]
rs8101046	0.80[EUR][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	esv3449420	chr19:45523560-45626884	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv912142	chr19:45570051-45708758	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv833842	chr19:45593888-45684308	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv833843	chr19:45593888-45793682	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12461416	Hs.466924	cis	multi-tissue	Pritchard
rs12461416	EIF5AP3	cis	lung	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45597400-45609400	Enhancers	Stomach Mucosa	stomach
2	chr19:45597600-45609200	Enhancers	Pancreas	Pancrea
3	chr19:45602000-45612200	Weak transcription	Hela-S3	cervix
4	chr19:45602800-45612600	Weak transcription	A549	lung
5	chr19:45603400-45609200	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr19:45603600-45609200	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr19:45603600-45612600	Weak transcription	Dnd41	blood
8	chr19:45603800-45619600	Weak transcription	HSMMtube	muscle
9	chr19:45604000-45609600	Enhancers	Fetal Muscle Leg	muscle
10	chr19:45604200-45609200	Enhancers	Spleen	Spleen
11	chr19:45604200-45611200	Weak transcription	K562	blood
12	chr19:45604600-45609200	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr19:45605200-45609200	Enhancers	Gastric	stomach
14	chr19:45605200-45609400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr19:45605800-45609400	Enhancers	Brain Hippocampus Middle	brain
16	chr19:45605800-45609400	Enhancers	Placenta	Placenta
17	chr19:45605800-45610000	Enhancers	Right Ventricle	heart
18	chr19:45606000-45609200	Enhancers	Primary hematopoietic stem cells	blood
19	chr19:45606600-45609400	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr19:45606600-45612600	Weak transcription	Ovary	ovary
21	chr19:45606600-45618000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr19:45606600-45623400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr19:45606600-45624800	Weak transcription	NHEK	skin
24	chr19:45606800-45609200	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr19:45606800-45609200	Enhancers	Fetal Thymus	thymus
26	chr19:45606800-45609400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr19:45606800-45609400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr19:45606800-45609400	Enhancers	Brain Substantia Nigra	brain
29	chr19:45606800-45610200	Weak transcription	Osteobl	bone
30	chr19:45606800-45612400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr19:45606800-45614200	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr19:45606800-45615200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:45606800-45616600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr19:45606800-45621000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr19:45606800-45634000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr19:45607000-45609200	Enhancers	Primary B cells from cord blood	blood
37	chr19:45607000-45609200	Enhancers	Primary T cells fromperipheralblood	blood
38	chr19:45607000-45609200	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr19:45607000-45611800	Enhancers	Primary B cells from peripheral blood	blood
40	chr19:45607200-45613800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr19:45607200-45616000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr19:45607200-45625600	Weak transcription	NHLF	lung
43	chr19:45607400-45609200	Enhancers	Brain Angular Gyrus	brain
44	chr19:45607400-45609200	Enhancers	Brain Cingulate Gyrus	brain
45	chr19:45607400-45612200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:45607600-45609200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:45607600-45610800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:45607600-45615800	Weak transcription	Fetal Lung	lung
49	chr19:45607600-45616000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr19:45607600-45626600	Weak transcription	Fetal Brain Male	brain

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