Variant report

Variant	rs12508599
Chromosome Location	chr4:160171509-160171510
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]
rs11100211	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11730876	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12502799	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12503790	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12507531	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12509160	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12509165	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13116575	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13119443	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13124646	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13152231	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56806866	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6536402	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67377365	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7659528	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9992208	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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	nsv830129	chr4:160061694-160270760	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12508599	RAPGEF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160133400-160171600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr4:160149400-160171800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:160149400-160172000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:160149400-160173000	Weak transcription	Placenta	Placenta
5	chr4:160149400-160216800	Weak transcription	Small Intestine	intestine
6	chr4:160149600-160171800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:160150600-160172000	Weak transcription	Lung	lung
8	chr4:160150800-160172000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:160151400-160171600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:160152000-160171800	Weak transcription	Fetal Intestine Large	intestine
11	chr4:160157400-160171800	Weak transcription	Fetal Intestine Small	intestine
12	chr4:160160600-160179800	Weak transcription	NHEK	skin
13	chr4:160162600-160172200	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr4:160162600-160177200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:160162800-160171600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:160164400-160178000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr4:160165200-160171600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr4:160166600-160176200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr4:160167200-160171800	Weak transcription	Spleen	Spleen
20	chr4:160167400-160186400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr4:160168800-160171800	Weak transcription	Right Ventricle	heart
22	chr4:160168800-160172000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr4:160169800-160172000	Weak transcription	Pancreas	Pancrea
24	chr4:160169800-160173200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr4:160169800-160175200	Weak transcription	Aorta	Aorta
26	chr4:160169800-160187800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr4:160170000-160171800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:160170000-160171800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:160170000-160171800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:160170000-160171800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr4:160170000-160187200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:160170200-160171800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:160170200-160171800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr4:160170200-160188000	Weak transcription	Fetal Kidney	kidney
35	chr4:160170400-160171800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:160170400-160171800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:160170400-160171800	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr4:160170400-160171800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr4:160170400-160171800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr4:160170400-160171800	Weak transcription	Fetal Muscle Leg	muscle
41	chr4:160170400-160171800	Weak transcription	Fetal Stomach	stomach
42	chr4:160170400-160171800	Weak transcription	Left Ventricle	heart
43	chr4:160170400-160171800	Weak transcription	Ovary	ovary
44	chr4:160170400-160172000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr4:160170400-160172200	Weak transcription	Fetal Brain Female	brain
46	chr4:160170400-160172400	Weak transcription	Fetal Heart	heart
47	chr4:160170400-160172600	Weak transcription	Liver	Liver
48	chr4:160170400-160173000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr4:160170400-160173000	Weak transcription	Fetal Lung	lung
50	chr4:160170400-160173200	Weak transcription	Brain Substantia Nigra	brain

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