Variant report

Variant	rs28562885
Chromosome Location	chr4:160206252-160206253
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10017696	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11100215	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12499444	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12507095	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13103075	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13145422	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13150322	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4295222	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6811571	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6816396	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6824247	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6824488	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6834008	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6835746	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847780	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6848217	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848706	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7349689	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9990664	0.96[AMR][1000 genomes];0.97[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
rs28562885	RAPGEF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160149400-160216800	Weak transcription	Small Intestine	intestine
2	chr4:160173200-160217400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:160186800-160225400	Weak transcription	Primary B cells from cord blood	blood
4	chr4:160189400-160235200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:160193400-160240200	Weak transcription	Gastric	stomach
6	chr4:160194200-160210000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:160194400-160209600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr4:160194400-160235600	Weak transcription	Fetal Stomach	stomach
9	chr4:160194400-160236600	Weak transcription	Primary T cells from cord blood	blood
10	chr4:160194600-160209400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:160195200-160209800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:160195200-160225600	Weak transcription	Placenta	Placenta
13	chr4:160200600-160235600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:160201800-160217200	Weak transcription	GM12878-XiMat	blood
15	chr4:160202800-160206400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:160202800-160206400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:160203200-160206400	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr4:160203400-160209600	Weak transcription	Psoas Muscle	Psoas
19	chr4:160203600-160216600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:160203800-160207800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr4:160204200-160207200	Enhancers	Brain Angular Gyrus	brain
22	chr4:160204800-160209200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:160205000-160206400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:160205200-160206400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr4:160205200-160216600	Weak transcription	Colon Smooth Muscle	Colon
26	chr4:160205400-160206400	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr4:160205400-160206600	Enhancers	A549	lung
28	chr4:160205400-160208600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:160205400-160209800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr4:160205400-160214800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr4:160205400-160218200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr4:160205400-160219000	Weak transcription	Fetal Intestine Small	intestine
33	chr4:160205600-160206400	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr4:160205600-160206600	Enhancers	NHEK	skin
35	chr4:160205600-160206800	Enhancers	NHLF	lung
36	chr4:160205600-160207400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr4:160205600-160207400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr4:160205600-160207800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr4:160205600-160207800	Weak transcription	Brain Hippocampus Middle	brain
40	chr4:160205600-160209000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr4:160205600-160209000	Weak transcription	Fetal Heart	heart
42	chr4:160205600-160209400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr4:160205600-160209600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr4:160205600-160209600	Weak transcription	Brain Substantia Nigra	brain
45	chr4:160205600-160209800	Weak transcription	Adipose Nuclei	Adipose
46	chr4:160205600-160209800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr4:160205600-160209800	Weak transcription	Ovary	ovary
48	chr4:160205600-160210400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:160205600-160217600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr4:160205800-160207800	Weak transcription	Liver	Liver

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