Variant report

Variant	rs13145422
Chromosome Location	chr4:160185669-160185670
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr4:160185400-160185725	SH-SY5Y	brain:	n/a	n/a
2	POLR2A	chr4:160185511-160185954	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:160175364..160178262-chr4:160184928..160186720,2	MCF-7	breast:
2	chr4:160184218..160186779-chr4:160192585..160194207,2	K562	blood:

Variant related genes	Relation type
RAPGEF2	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10017696	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11100215	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12499444	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12507095	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13103075	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13150322	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28562885	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4295222	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6811571	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6816396	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6824247	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6824488	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834008	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6835746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6847780	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6848217	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6848706	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7349689	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7699824	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9990664	0.94[AMR][1000 genomes];0.91[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13145422	GRIA2	cis	cerebellum	SCAN
rs13145422	RAPGEF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160149400-160216800	Weak transcription	Small Intestine	intestine
2	chr4:160167400-160186400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:160169800-160187800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:160170000-160187200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:160170200-160188000	Weak transcription	Fetal Kidney	kidney
6	chr4:160170400-160186400	Weak transcription	Fetal Brain Male	brain
7	chr4:160170400-160188000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr4:160170400-160188400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr4:160170400-160192800	Weak transcription	Primary T cells from cord blood	blood
10	chr4:160170600-160188000	Weak transcription	Osteobl	bone
11	chr4:160170600-160188200	Weak transcription	Psoas Muscle	Psoas
12	chr4:160172600-160188200	Weak transcription	Pancreas	Pancrea
13	chr4:160172600-160193000	Weak transcription	Gastric	stomach
14	chr4:160173000-160193200	Weak transcription	Thymus	Thymus
15	chr4:160173200-160187800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:160173200-160188200	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr4:160173200-160188600	Weak transcription	Lung	lung
18	chr4:160173200-160192400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:160173200-160217400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:160173400-160188000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr4:160173400-160188000	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr4:160173400-160188000	Weak transcription	Fetal Stomach	stomach
23	chr4:160173400-160188000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:160173400-160188200	Weak transcription	Right Ventricle	heart
25	chr4:160173400-160188400	Weak transcription	Fetal Muscle Leg	muscle
26	chr4:160173400-160188400	Weak transcription	GM12878-XiMat	blood
27	chr4:160173400-160188400	Weak transcription	HSMM	muscle
28	chr4:160173400-160192600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr4:160173400-160194000	Weak transcription	Fetal Intestine Large	intestine
30	chr4:160173400-160194800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr4:160173600-160188400	Weak transcription	Fetal Intestine Small	intestine
32	chr4:160174000-160203400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:160174600-160186200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:160175400-160186400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:160176400-160186000	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr4:160177600-160185800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:160177600-160187800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:160178600-160186600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr4:160178600-160187200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:160178600-160188600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr4:160178800-160188200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr4:160179000-160187400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:160180200-160192600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:160181400-160186200	Weak transcription	Left Ventricle	heart
45	chr4:160181600-160188000	Weak transcription	Liver	Liver
46	chr4:160183200-160187400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr4:160183400-160187800	Weak transcription	Brain Substantia Nigra	brain
48	chr4:160183600-160186200	Weak transcription	HUVEC	blood vessel
49	chr4:160183600-160187800	Weak transcription	NHLF	lung
50	chr4:160183800-160187200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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