Variant report

Variant	rs7349689
Chromosome Location	chr4:160232403-160232404
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10017696	0.96[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11100215	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12499444	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12507095	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13103075	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13145422	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13150322	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28562885	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4295222	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6811571	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6816396	0.96[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6824247	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6824488	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6834008	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6835746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847780	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6848217	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848706	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7699824	1.00[YRI][hapmap]
rs9990664	0.96[AMR][1000 genomes];0.90[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
rs7349689	RAPGEF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160189400-160235200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr4:160193400-160240200	Weak transcription	Gastric	stomach
3	chr4:160194400-160235600	Weak transcription	Fetal Stomach	stomach
4	chr4:160194400-160236600	Weak transcription	Primary T cells from cord blood	blood
5	chr4:160200600-160235600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:160205800-160236400	Weak transcription	Pancreas	Pancrea
7	chr4:160205800-160260600	Weak transcription	Aorta	Aorta
8	chr4:160210600-160238000	Weak transcription	Adipose Nuclei	Adipose
9	chr4:160215200-160236800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr4:160216600-160237600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr4:160217000-160259400	Weak transcription	Fetal Brain Male	brain
12	chr4:160220000-160232600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:160220000-160244400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr4:160223000-160260000	Weak transcription	Ovary	ovary
15	chr4:160224400-160236400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr4:160224600-160235800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr4:160224600-160262400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr4:160225000-160236600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:160225200-160260200	Weak transcription	Thymus	Thymus
20	chr4:160225400-160236400	Weak transcription	Fetal Intestine Small	intestine
21	chr4:160225600-160253600	Weak transcription	HepG2	liver
22	chr4:160226000-160260800	Weak transcription	Colonic Mucosa	Colon
23	chr4:160226200-160235200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr4:160226200-160235800	Weak transcription	Fetal Muscle Leg	muscle
25	chr4:160226200-160244000	Weak transcription	Fetal Kidney	kidney
26	chr4:160226200-160270600	Weak transcription	Small Intestine	intestine
27	chr4:160226400-160235800	Weak transcription	Placenta	Placenta
28	chr4:160226400-160242400	Weak transcription	GM12878-XiMat	blood
29	chr4:160226600-160235800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr4:160226600-160237600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr4:160227000-160235000	Weak transcription	Primary B cells from cord blood	blood
32	chr4:160227200-160235600	Weak transcription	Fetal Intestine Large	intestine
33	chr4:160227200-160235800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr4:160227200-160236400	Weak transcription	Fetal Lung	lung
35	chr4:160229000-160242600	Weak transcription	Right Atrium	heart
36	chr4:160229200-160236600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr4:160229200-160247600	Weak transcription	Stomach Mucosa	stomach
38	chr4:160229400-160232600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:160229800-160233400	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr4:160229800-160235800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:160230000-160251800	Weak transcription	NHDF-Ad	bronchial
42	chr4:160230200-160235800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:160230200-160236800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr4:160230200-160239200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:160230200-160263800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:160230200-160270800	Weak transcription	A549	lung
47	chr4:160230400-160235600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:160230400-160235800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr4:160230400-160235800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr4:160230400-160236600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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