Variant report

Variant	rs12507531
Chromosome Location	chr4:160170661-160170662
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11100211	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11730876	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12502799	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12503790	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508599	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12509160	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12509165	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13116575	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13119443	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13124646	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13152231	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56806866	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6536402	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67377365	0.87[EUR][1000 genomes]
rs7659528	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9992208	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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
rs12507531	RAPGEF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 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	chr4:160149400-160171800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:160149400-160172000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:160149400-160173000	Weak transcription	Placenta	Placenta
5	chr4:160149400-160216800	Weak transcription	Small Intestine	intestine
6	chr4:160149600-160171800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:160150600-160172000	Weak transcription	Lung	lung
8	chr4:160150800-160172000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:160151400-160171600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:160152000-160171800	Weak transcription	Fetal Intestine Large	intestine
11	chr4:160154800-160171400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr4:160157400-160171800	Weak transcription	Fetal Intestine Small	intestine
13	chr4:160159400-160171000	Weak transcription	GM12878-XiMat	blood
14	chr4:160160600-160179800	Weak transcription	NHEK	skin
15	chr4:160162600-160172200	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr4:160162600-160177200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:160162800-160171600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr4:160164400-160178000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr4:160165200-160171200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:160165200-160171600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr4:160166600-160176200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr4:160167200-160171800	Weak transcription	Spleen	Spleen
23	chr4:160167400-160186400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr4:160168800-160171800	Weak transcription	Right Ventricle	heart
25	chr4:160168800-160172000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr4:160169800-160170800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:160169800-160172000	Weak transcription	Pancreas	Pancrea
28	chr4:160169800-160173200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr4:160169800-160175200	Weak transcription	Aorta	Aorta
30	chr4:160169800-160187800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr4:160170000-160171800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:160170000-160171800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:160170000-160171800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:160170000-160171800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:160170000-160187200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr4:160170200-160171800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:160170200-160171800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr4:160170200-160188000	Weak transcription	Fetal Kidney	kidney
39	chr4:160170400-160170800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:160170400-160171200	Enhancers	Brain Anterior Caudate	brain
41	chr4:160170400-160171400	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr4:160170400-160171800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:160170400-160171800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:160170400-160171800	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr4:160170400-160171800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:160170400-160171800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr4:160170400-160171800	Weak transcription	Fetal Muscle Leg	muscle
48	chr4:160170400-160171800	Weak transcription	Fetal Stomach	stomach
49	chr4:160170400-160171800	Weak transcription	Left Ventricle	heart
50	chr4:160170400-160171800	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links