Variant report

Variant	rs10412988
Chromosome Location	chr19:45612774-45612775
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:45612595..45615148-chr19:45656372..45657898,2	K562	blood:
2	chr19:45611547..45614540-chr19:45634096..45635965,2	K562	blood:
3	chr19:45611325..45613893-chr19:45616421..45619737,3	K562	blood:
4	chr19:45603847..45605776-chr19:45612544..45615012,2	K562	blood:

Variant related genes	Relation type
ENSG00000179846	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10403214	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10405306	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10405719	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10405721	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10407374	1.00[EUR][1000 genomes]
rs10408366	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10409138	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs10409232	0.91[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10409727	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10409903	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10410424	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10417101	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10417618	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10417804	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10421932	0.92[CEU][hapmap]
rs10424651	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12459945	0.80[EUR][1000 genomes]
rs12461416	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1541926	1.00[EUR][1000 genomes]
rs17562676	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17562787	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17642665	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1982077	1.00[EUR][1000 genomes]
rs2011438	0.80[EUR][1000 genomes]
rs4608431	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4803798	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4803799	0.97[ASN][1000 genomes]
rs7257566	0.98[EUR][1000 genomes]
rs7257599	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73034821	0.97[ASN][1000 genomes]
rs733289	1.00[CEU][hapmap];0.83[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]
rs999559	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[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	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
rs10412988	EIF5AP3	cis	lung	GTEx
rs10412988	Hs.466924	cis	multi-tissue	Pritchard

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45603800-45619600	Weak transcription	HSMMtube	muscle
2	chr19:45606600-45618000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr19:45606600-45623400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:45606600-45624800	Weak transcription	NHEK	skin
5	chr19:45606800-45614200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr19:45606800-45615200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:45606800-45616600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr19:45606800-45621000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:45606800-45634000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr19:45607200-45613800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr19:45607200-45616000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr19:45607200-45625600	Weak transcription	NHLF	lung
13	chr19:45607600-45615800	Weak transcription	Fetal Lung	lung
14	chr19:45607600-45616000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr19:45607600-45626600	Weak transcription	Fetal Brain Male	brain
16	chr19:45607800-45620400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:45607800-45620600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr19:45608000-45616600	Weak transcription	Brain Anterior Caudate	brain
19	chr19:45608000-45616800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr19:45608000-45618400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:45608000-45619800	Weak transcription	Brain Germinal Matrix	brain
22	chr19:45608000-45620800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr19:45608000-45639400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr19:45608200-45614000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr19:45608200-45616600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:45608200-45619800	Weak transcription	Adipose Nuclei	Adipose
27	chr19:45608400-45613800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr19:45608400-45614600	Weak transcription	Small Intestine	intestine
29	chr19:45608400-45615600	Weak transcription	HepG2	liver
30	chr19:45608400-45616600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:45608400-45616600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr19:45608400-45629200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr19:45608600-45618600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr19:45608600-45619400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:45608600-45619600	Weak transcription	Psoas Muscle	Psoas
36	chr19:45608600-45621000	Weak transcription	Fetal Brain Female	brain
37	chr19:45608800-45613000	Weak transcription	Lung	lung
38	chr19:45608800-45613800	Weak transcription	Left Ventricle	heart
39	chr19:45608800-45615600	Weak transcription	Primary T cells from cord blood	blood
40	chr19:45608800-45615600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr19:45608800-45618600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr19:45608800-45618600	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr19:45608800-45619600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr19:45609000-45616200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr19:45609000-45616400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:45609000-45618600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr19:45609000-45621400	Weak transcription	Right Atrium	heart
48	chr19:45609200-45612800	Weak transcription	Fetal Thymus	thymus
49	chr19:45609200-45613600	Weak transcription	Pancreas	Pancrea
50	chr19:45609200-45613800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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