Variant report

Variant	rs2017052
Chromosome Location	chr4:160244212-160244213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:160241453..160244451-chr4:160244755..160246278,2	K562	blood:

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10022399	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11723634	0.83[EUR][1000 genomes]
rs11727094	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13127789	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13147632	0.82[EUR][1000 genomes]
rs3749465	0.83[EUR][1000 genomes]
rs6536412	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv1022771	chr4:160188801-160324683	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2017052	RAPGEF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160205800-160260600	Weak transcription	Aorta	Aorta
2	chr4:160217000-160259400	Weak transcription	Fetal Brain Male	brain
3	chr4:160220000-160244400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr4:160223000-160260000	Weak transcription	Ovary	ovary
5	chr4:160224600-160262400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:160225200-160260200	Weak transcription	Thymus	Thymus
7	chr4:160225600-160253600	Weak transcription	HepG2	liver
8	chr4:160226000-160260800	Weak transcription	Colonic Mucosa	Colon
9	chr4:160226200-160270600	Weak transcription	Small Intestine	intestine
10	chr4:160229200-160247600	Weak transcription	Stomach Mucosa	stomach
11	chr4:160230000-160251800	Weak transcription	NHDF-Ad	bronchial
12	chr4:160230200-160263800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:160230200-160270800	Weak transcription	A549	lung
14	chr4:160230400-160253600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:160230400-160259400	Weak transcription	NHLF	lung
16	chr4:160230400-160260200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:160230400-160260600	Weak transcription	HSMMtube	muscle
18	chr4:160230600-160260000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:160231000-160259400	Weak transcription	HMEC	breast
20	chr4:160231000-160260400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:160231000-160260400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr4:160232200-160274600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr4:160232800-160253400	Weak transcription	Psoas Muscle	Psoas
24	chr4:160233000-160253400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr4:160233000-160260000	Weak transcription	Colon Smooth Muscle	Colon
26	chr4:160233600-160259600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr4:160233800-160264000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr4:160234000-160259400	Weak transcription	Esophagus	oesophagus
29	chr4:160234200-160260200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:160235000-160248200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr4:160235200-160248200	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr4:160235200-160266200	Weak transcription	Spleen	Spleen
33	chr4:160236000-160252600	Weak transcription	Osteobl	bone
34	chr4:160236000-160259400	Weak transcription	Brain Angular Gyrus	brain
35	chr4:160236800-160260200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr4:160237000-160279400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr4:160237000-160284400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr4:160237200-160252600	Weak transcription	Brain Substantia Nigra	brain
39	chr4:160237200-160254200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr4:160237400-160244600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr4:160237400-160266200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:160237400-160274600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr4:160237600-160260000	Weak transcription	Fetal Thymus	thymus
44	chr4:160238200-160260000	Weak transcription	Fetal Brain Female	brain
45	chr4:160238400-160244400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr4:160238600-160260200	Weak transcription	Pancreas	Pancrea
47	chr4:160238600-160263800	Weak transcription	Fetal Stomach	stomach
48	chr4:160238600-160263800	Weak transcription	Lung	lung
49	chr4:160238600-160282200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr4:160238800-160244800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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