Variant report

Variant	rs12505801
Chromosome Location	chr4:99554312-99554313
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10034419	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12507328	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1528545	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2866014	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs28713515	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6532755	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6837798	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6837860	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6837959	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7661136	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7671702	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7686325	0.94[ASN][1000 genomes]
rs871473	0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs871474	0.80[CHD][hapmap]
rs9307228	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9991053	0.92[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594940	chr4:99542475-99573350	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12505801	EIF4E	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99546600-99560000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr4:99546800-99559800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr4:99547200-99554400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr4:99547800-99559200	Weak transcription	Stomach Mucosa	stomach
5	chr4:99548000-99560600	Weak transcription	Right Atrium	heart
6	chr4:99548000-99569200	Weak transcription	Gastric	stomach
7	chr4:99548000-99577000	Weak transcription	Esophagus	oesophagus
8	chr4:99548400-99563600	Weak transcription	HSMM	muscle
9	chr4:99549600-99563200	Weak transcription	HMEC	breast
10	chr4:99549800-99563600	Weak transcription	NHEK	skin
11	chr4:99550000-99563600	Weak transcription	HUVEC	blood vessel
12	chr4:99550400-99554800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:99550600-99555000	Enhancers	Fetal Brain Male	brain
14	chr4:99551000-99554600	Enhancers	Brain Cingulate Gyrus	brain
15	chr4:99551200-99554400	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr4:99551400-99554400	Enhancers	Brain Anterior Caudate	brain
17	chr4:99551400-99554400	Enhancers	Ovary	ovary
18	chr4:99551600-99555000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:99551800-99563200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:99552200-99559400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr4:99552400-99556000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr4:99552600-99569600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr4:99552800-99559200	Weak transcription	Placenta	Placenta
24	chr4:99552800-99560000	Weak transcription	Thymus	Thymus
25	chr4:99552800-99560200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr4:99552800-99569200	Weak transcription	Fetal Stomach	stomach
27	chr4:99553000-99559200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr4:99553000-99559400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr4:99553200-99559400	Weak transcription	NHLF	lung
30	chr4:99553200-99564200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:99553400-99554400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr4:99553600-99557400	Weak transcription	Fetal Heart	heart
33	chr4:99553600-99560000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr4:99553800-99556400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:99554000-99554400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:99554000-99558000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr4:99554000-99558400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:99554000-99564000	Weak transcription	Osteobl	bone
39	chr4:99554200-99554400	Enhancers	Fetal Brain Female	brain
40	chr4:99554200-99556000	Weak transcription	Brain Hippocampus Middle	brain
41	chr4:99554200-99556400	Weak transcription	Brain Angular Gyrus	brain
42	chr4:99554200-99558000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:99554200-99558000	Weak transcription	Brain Substantia Nigra	brain
44	chr4:99554200-99558200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr4:99554200-99558400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr4:99554200-99559200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr4:99554200-99559200	Weak transcription	NHDF-Ad	bronchial
48	chr4:99554200-99562600	Weak transcription	NH-A	brain
49	chr4:99554200-99564200	Weak transcription	Pancreas	Pancrea
50	chr4:99554200-99569200	Weak transcription	Spleen	Spleen

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