Variant report

Variant	rs6536402
Chromosome Location	chr4:160152565-160152566
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11100211	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11730876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12502799	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12503790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507531	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508599	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12509160	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12509165	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13116575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13119443	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13124646	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13152231	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56806866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67377365	0.87[EUR][1000 genomes]
rs7659528	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9992208	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016150	chr4:159995816-160165156	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	7 gene(s)	inside rSNPs	diseases
2	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
3	esv1795614	chr4:160142544-160161916	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6536402	RAPGEF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 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	chr4:160134200-160156600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr4:160138000-160156000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:160149000-160153000	Active TSS	Right Ventricle	heart
5	chr4:160149400-160164000	Weak transcription	K562	blood
6	chr4:160149400-160169600	Weak transcription	Pancreas	Pancrea
7	chr4:160149400-160171800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:160149400-160172000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:160149400-160173000	Weak transcription	Placenta	Placenta
10	chr4:160149400-160216800	Weak transcription	Small Intestine	intestine
11	chr4:160149600-160171800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:160149800-160154200	Weak transcription	Liver	Liver
13	chr4:160149800-160154400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:160150400-160153400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:160150600-160153600	Weak transcription	Psoas Muscle	Psoas
16	chr4:160150600-160172000	Weak transcription	Lung	lung
17	chr4:160150800-160153800	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr4:160150800-160154400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr4:160150800-160156400	Weak transcription	Brain Anterior Caudate	brain
20	chr4:160150800-160156400	Weak transcription	HepG2	liver
21	chr4:160150800-160158200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:160150800-160162200	Weak transcription	NHDF-Ad	bronchial
23	chr4:160150800-160162400	Weak transcription	Brain Angular Gyrus	brain
24	chr4:160150800-160168400	Weak transcription	NH-A	brain
25	chr4:160150800-160172000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:160151000-160154200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr4:160151200-160153400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr4:160151200-160153800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr4:160151200-160159600	Weak transcription	HSMM	muscle
30	chr4:160151200-160160400	Weak transcription	Brain Hippocampus Middle	brain
31	chr4:160151400-160153600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr4:160151400-160159800	Weak transcription	Brain Substantia Nigra	brain
33	chr4:160151400-160171600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:160151800-160153600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:160151800-160162000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:160152000-160153000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr4:160152000-160155800	Weak transcription	Left Ventricle	heart
38	chr4:160152000-160156400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr4:160152000-160157000	Weak transcription	Fetal Intestine Small	intestine
40	chr4:160152000-160158200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr4:160152000-160159600	Weak transcription	NHEK	skin
42	chr4:160152000-160162800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr4:160152000-160171800	Weak transcription	Fetal Intestine Large	intestine
44	chr4:160152200-160153400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:160152200-160153600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr4:160152200-160160400	Weak transcription	Colon Smooth Muscle	Colon
47	chr4:160152200-160169400	Weak transcription	NHLF	lung
48	chr4:160152400-160153000	Weak transcription	Fetal Heart	heart
49	chr4:160152400-160153400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr4:160152400-160153600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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