Variant report

Variant	rs7699824
Chromosome Location	chr4:160187731-160187732
allele	A/T
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:20)

rs_ID	r²[population]
rs10017696	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11100215	0.89[AMR][1000 genomes]
rs12499444	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12507095	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13103075	0.91[AMR][1000 genomes]
rs13145422	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13150322	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28562885	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4295222	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6811571	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6816396	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs6824247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs6824488	1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6834008	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6835746	1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs6847780	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6848217	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6848706	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7349689	1.00[YRI][hapmap];0.92[AMR][1000 genomes]
rs9990664	0.89[AMR][1000 genomes];0.83[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
rs7699824	RAPGEF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160149400-160216800	Weak transcription	Small Intestine	intestine
2	chr4:160169800-160187800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:160170200-160188000	Weak transcription	Fetal Kidney	kidney
4	chr4:160170400-160188000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr4:160170400-160188400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr4:160170400-160192800	Weak transcription	Primary T cells from cord blood	blood
7	chr4:160170600-160188000	Weak transcription	Osteobl	bone
8	chr4:160170600-160188200	Weak transcription	Psoas Muscle	Psoas
9	chr4:160172600-160188200	Weak transcription	Pancreas	Pancrea
10	chr4:160172600-160193000	Weak transcription	Gastric	stomach
11	chr4:160173000-160193200	Weak transcription	Thymus	Thymus
12	chr4:160173200-160187800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr4:160173200-160188200	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr4:160173200-160188600	Weak transcription	Lung	lung
15	chr4:160173200-160192400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:160173200-160217400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:160173400-160188000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr4:160173400-160188000	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr4:160173400-160188000	Weak transcription	Fetal Stomach	stomach
20	chr4:160173400-160188000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:160173400-160188200	Weak transcription	Right Ventricle	heart
22	chr4:160173400-160188400	Weak transcription	Fetal Muscle Leg	muscle
23	chr4:160173400-160188400	Weak transcription	GM12878-XiMat	blood
24	chr4:160173400-160188400	Weak transcription	HSMM	muscle
25	chr4:160173400-160192600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr4:160173400-160194000	Weak transcription	Fetal Intestine Large	intestine
27	chr4:160173400-160194800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:160173600-160188400	Weak transcription	Fetal Intestine Small	intestine
29	chr4:160174000-160203400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr4:160177600-160187800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr4:160178600-160188600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr4:160178800-160188200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr4:160180200-160192600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:160181600-160188000	Weak transcription	Liver	Liver
35	chr4:160183400-160187800	Weak transcription	Brain Substantia Nigra	brain
36	chr4:160183600-160187800	Weak transcription	NHLF	lung
37	chr4:160183800-160187800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr4:160183800-160188000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:160183800-160188000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:160183800-160188000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr4:160183800-160188000	Weak transcription	NHDF-Ad	bronchial
42	chr4:160184000-160187800	Weak transcription	Brain Hippocampus Middle	brain
43	chr4:160184200-160188000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:160184200-160188000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:160184400-160187800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:160185200-160188000	Weak transcription	Brain Angular Gyrus	brain
47	chr4:160186000-160188000	Weak transcription	Right Atrium	heart
48	chr4:160186000-160196400	Enhancers	Fetal Heart	heart
49	chr4:160186200-160188000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr4:160186200-160188200	Enhancers	HUVEC	blood vessel

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